forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5131 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
2b36a041bc
commit
c936d176fc
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@ -384,16 +384,16 @@ potentials. Click on the style itself for a full description:
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<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
|
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<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
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</TD></TR></TABLE></DIV>
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<P>These are pair styles contributed by users, which can be used if
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@ -426,8 +426,8 @@ angle potentials. Click on the style itself for a full description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD></TR>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
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</TD></TR></TABLE></DIV>
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<P>These are angle styles contributed by users, which can be used if
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@ -460,7 +460,7 @@ description:
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A>
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<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
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</TD></TR></TABLE></DIV>
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<HR>
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@ -579,6 +579,8 @@ potentials. Click on the style itself for a full description:
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"gran/hertz/history"_pair_gran.html,
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"gran/hooke"_pair_gran.html,
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"gran/hooke/history"_pair_gran.html,
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"hbond/dreiding/lj"_pair_hbond_dreiding.html,
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"hbond/dreiding/morse"_pair_hbond_dreiding.html,
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"lj/charmm/coul/charmm"_pair_charmm.html,
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"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
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"lj/charmm/coul/long"_pair_charmm.html,
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@ -657,6 +659,7 @@ angle potentials. Click on the style itself for a full description:
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"class2"_angle_class2.html,
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"cosine"_angle_cosine.html,
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"cosine/delta"_angle_cosine_delta.html,
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"cosine/periodic"_angle_cosine_periodic.html,
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"cosine/squared"_angle_cosine_squared.html,
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"harmonic"_angle_harmonic.html,
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"table"_angle_table.html :tb(c=4,ea=c,w=100)
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@ -695,7 +698,8 @@ description:
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"hybrid"_improper_hybrid.html,
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"class2"_improper_class2.html,
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"cvff"_improper_cvff.html,
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"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100)
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"harmonic"_improper_harmonic.html,
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"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
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:line
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@ -16,7 +16,7 @@ certain kinds of LAMMPS simulations.
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</P>
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4.1 <A HREF = "#4_1">Restarting a simulation</A><BR>
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4.2 <A HREF = "#4_2">2d simulations</A><BR>
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4.3 <A HREF = "#4_3">CHARMM and AMBER force fields</A><BR>
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4.3 <A HREF = "#4_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
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4.4 <A HREF = "#4_4">Running multiple simulations from one input script</A><BR>
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4.5 <A HREF = "#4_5">Multi-replica simulations</A><BR>
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4.6 <A HREF = "#4_6">Granular models</A><BR>
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@ -31,8 +31,7 @@ certain kinds of LAMMPS simulations.
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4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
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4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A><BR>
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4.17 <A HREF = "#4_17">Walls</A><BR>
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4.18 <A HREF = "#4_18">Elastic constants</A><BR>
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4.19 <A HREF = "#4_19">Computing free energies from thermodyanmic integration</A> <BR>
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4.18 <A HREF = "#4_18">Elastic constants</A> <BR>
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<P>The example input scripts included in the LAMMPS distribution and
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highlighted in <A HREF = "Section_example.html">this section</A> also show how to
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@ -167,19 +166,18 @@ the same as in 3d.
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</P>
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<HR>
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<A NAME = "4_3"></A><H4>4.3 CHARMM and AMBER force fields
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<A NAME = "4_3"></A><H4>4.3 CHARMM, AMBER, and DREIDING force fields
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</H4>
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<P>There are many different ways to compute forces in the <A HREF = "http://www.scripps.edu/brooks">CHARMM</A>
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and <A HREF = "http://amber.scripps.edu">AMBER</A> molecular dynamics codes, only some of which are
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available as options in LAMMPS. A force field has 2 parts: the
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formulas that define it and the coefficients used for a particular
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system. Here we only discuss formulas implemented in LAMMPS. Setting
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<P>A force field has 2 parts: the formulas that define it and the
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coefficients used for a particular system. Here we only discuss
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formulas implemented in LAMMPS that correspond to formulas commonly
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used in the CHARMM, AMBER, and DREIDING force fields. Setting
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coefficients is done in the input data file via the
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<A HREF = "read_data.html">read_data</A> command or in the input script with
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commands like <A HREF = "pair_coeff.html">pair_coeff</A> or
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<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A> for
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additional tools that can use CHARMM or AMBER to assign force field
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coefficients and convert their output into LAMMPS input.
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<A HREF = "bond_coeff.html">bond_coeff</A>. See <A HREF = "Section_tools.html">this section</A>
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for additional tools that can use CHARMM or AMBER to assign force
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field coefficients and convert their output into LAMMPS input.
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</P>
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<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
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field. See <A HREF = "#Cornell">(Cornell)</A> for a description of the AMBER force
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@ -193,16 +191,56 @@ field.
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with common options in CHARMM or AMBER. See each command's
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documentation for the formula it computes.
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</P>
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<UL><LI><A HREF = "bond_style.html">bond_style</A> harmonic
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<LI><A HREF = "angle_style.html">angle_style</A> charmm
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<LI><A HREF = "dihedral_style.html">dihedral_style</A> charmm
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/charmm/implicit
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<LI><A HREF = "pair_style.html">pair_style</A> lj/charmm/coul/long
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<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
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<LI><A HREF = "angle_charmm.html">angle_style</A> charmm
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<LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
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<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm
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<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/charmm/implicit
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<LI><A HREF = "pair_charmm.html">pair_style</A> lj/charmm/coul/long
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</UL>
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<UL><LI><A HREF = "special_bonds.html">special_bonds</A> charmm
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<LI><A HREF = "special_bonds.html">special_bonds</A> amber
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</UL>
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<P>DREIDING is a generic force field developed by the <A HREF = "http://www.wag.caltech.edu">Goddard
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group</A> at Caltech and is useful for
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predicting structures and dynamics of organic, biological and
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main-group inorganic molecules. The philosophy in DREIDING is to use
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general force constants and geometry parameters based on simple
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hybridization considerations, rather than individual force constants
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and geometric parameters that depend on the particular combinations of
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atoms involved in the bond, angle, or torsion terms. DREIDING has an
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<A HREF = "pair_hbond_dreiding.html">explicit hydrogen bond term</A> to describe
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interactions involving a hydrogen atom (H___A) on very electronegative
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atoms (N, O, F).
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</P>
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<P>See <A HREF = "#Mayo">(Mayo)</A> for a description of the DREIDING force field
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</P>
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<P>These style choices compute force field formulas that are consistent
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with the DREIDING force field. See each command's
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documentation for the formula it computes.
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</P>
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<UL><LI><A HREF = "bond_harmonic.html">bond_style</A> harmonic
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<LI><A HREF = "bond_morse.html">bond_style</A> morse
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</UL>
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<UL><LI><A HREF = "angle_harmonic.html">angle_style</A> harmonic
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<LI><A HREF = "angle_cosine.html">angle_style</A> cosine
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<LI><A HREF = "angle_cosine_periodic.html">angle_style</A> cosine/periodic
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</UL>
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<UL><LI><A HREF = "dihedral_charmm.html">dihedral_style</A> charmm
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<LI><A HREF = "improper_umbrella.html">improper_style</A> umbrella
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</UL>
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<UL><LI><A HREF = "pair_buck.html">pair_style</A> buck
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<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/cut
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<LI><A HREF = "pair_buck.html">pair_style</A> buck/coul/long
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<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut
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<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/cut
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<LI><A HREF = "pair_lj.html">pair_style</A> lj/cut/coul/long
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</UL>
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<UL><LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/lj
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<LI><A HREF = "pair_hbond_dreiding.html">pair_style</A> hbond/dreiding/morse
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</UL>
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<UL><LI><A HREF = "special_bonds.html">special_bonds</A> dreiding
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</UL>
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<HR>
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<A NAME = "4_4"></A><H4>4.4 Running multiple simulations from one input script
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@ -1610,72 +1648,6 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
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</P>
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<HR>
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<A NAME = "4_19"></A><H4>4.19 Computing free energies from thermodynamic integration
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</H4>
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<P>Thermodynamic integration is a widely used method to compute free
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energies from atomistic simulations. LAMMPS can be used to run
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thermodynamic integration calculations using the methods discussed in
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this section and the <A HREF = "fix_adapt.html">fix adapt</A> command. Currently,
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it is capable of the transformations essential for computing melting
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points using the pseudo-supercritical path method developed by <A HREF = "#Eike_Maginn">Eike
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and Maginn</A>.
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</P>
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<P>See the examples/TI directory for more information and sample files
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that compute a melting point using the techniques described in this
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section. That directory has its own README file. See also the paper
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by <A HREF = "#Jayaraman">Jayaraman</A> for an example of using this implementation
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of thermodynamic integration in LAMMPS to compute melting points of
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alkali nitrate salts, using the steps outlined here.
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</P>
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<P>In this method, three intermediate "pseudo-supercritical" states are
|
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accessed in the transformation between the liquid and solid
|
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phases. These pseudo-states are a weak liquid, a dense weak liquid,
|
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and an ordered weak phase. The transformation between the liquid and
|
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solid states can also be driven uisng the <A HREF = "fix_adapt.html">fix adapt</A>
|
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command.
|
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</P>
|
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<P>For the transformation from the liquid to the weak phase, the
|
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intermolecular interactions need to be weakened. Appropriate scale
|
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factors, computed by variables you define, and applied to pair styles
|
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by <A HREF = "fix_adapt.html">fix adapt</A>, can be used to do this, as in the
|
||||
example scripts. The <A HREF = "compute_ti.html">compute ti</A> command can
|
||||
accumulate the value of dU/d<I>lambda</I>. See <A HREF = "#Jayaraman_Maginn">Jayaraman and
|
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Maginn</A> for more information about calculating a
|
||||
free energy from dU/d<I>lambda</I>.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
|
||||
are listed on the <A HREF = "fix_adapt">fix adapt</A> doc page. interaction scaling
|
||||
is desired. If a pair style is not on that list, it is generally
|
||||
quite easy to add an extract() method to the pair style, to enable fix
|
||||
adapt to rescale it.
|
||||
</P>
|
||||
<P>Step 2 is the transformation of the simulation box density from the
|
||||
liquid phase to that of the equilibrated crystal. The parameters for
|
||||
box1 and box2 should be obtained from equilibrated NPT simulations of
|
||||
the liquid and crystal phases and used in a <A HREF = "fix_deform.html">fix
|
||||
deform</A> command to change the box size and/or shape.
|
||||
It also advisable to use <A HREF = "fix_adapt.html">fix adapt</A> on the pair styles
|
||||
to prevent overlaps which may occur during the box transformation.
|
||||
</P>
|
||||
<P>In step 3, the dense, weak system is transformed to an ordered state,
|
||||
which has the same ordering as in the equilibrated crystal. Ordering
|
||||
is achieved by introducing an attractive potential between atoms and
|
||||
lattice sites. These lattice sites can be calculated as the mean
|
||||
positions of the atoms in an equilibrium simulation of the
|
||||
crystal. The <A HREF = "pair_gauss.html">pair/gauss</A> command can be used to
|
||||
introduce an attractive Gaussian potential between the atoms and their
|
||||
corresponding lattice sites. The prefactor of the Gaussian pair
|
||||
potential can be scaled by <A HREF = "fix_adapt.html">fix adapt</A> to turn on the
|
||||
attractions. Again, the quantity dU/d<I>lambda</I> can be tracked via the
|
||||
<A HREF = "compute_ti.html">compute ti</A> command.
|
||||
</P>
|
||||
<P>Step 4 is the transformation of the ordered state to the final
|
||||
crystal. In this step, the intermolecular interactions are scaled
|
||||
back to full strength, while the Gaussian tethers are removed, all via
|
||||
<A HREF = "fix_adapt.html">fix adapt</A>.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "Berendsen"></A>
|
||||
|
|
@ -1698,6 +1670,11 @@ J Chem Phys, 120, 9665 (2004).
|
|||
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
</P>
|
||||
<A NAME = "Mayo"></A>
|
||||
|
||||
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
</P>
|
||||
<A NAME = "Jorgensen"></A>
|
||||
|
||||
<P><B>(Jorgensen)</B> Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||
|
|
@ -1711,19 +1688,4 @@ Phys, 79, 926 (1983).
|
|||
|
||||
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
</P>
|
||||
<A NAME = "Eike_Maginn"></A>
|
||||
|
||||
<P><B>(Eike and Maginn)</B> Eike and Maginn, J Chem Phys, 124,
|
||||
164503 (2006).
|
||||
</P>
|
||||
<A NAME = "Jayaraman_Maginn"></A>
|
||||
|
||||
<P><B>(Jayaraman and Maginn)</B> Jayaraman and Maginn, Journal of Chemical Physics,
|
||||
127, 214504 (2007).
|
||||
</P>
|
||||
<A NAME = "Jayaraman"></A>
|
||||
|
||||
<P><B>(Jayaraman)</B> Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
|
||||
and Engineering Chemistry Research, 49, 559-571 (2010).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ certain kinds of LAMMPS simulations.
|
|||
|
||||
4.1 "Restarting a simulation"_#4_1
|
||||
4.2 "2d simulations"_#4_2
|
||||
4.3 "CHARMM and AMBER force fields"_#4_3
|
||||
4.3 "CHARMM, AMBER, and DREIDING force fields"_#4_3
|
||||
4.4 "Running multiple simulations from one input script"_#4_4
|
||||
4.5 "Multi-replica simulations"_#4_5
|
||||
4.6 "Granular models"_#4_6
|
||||
|
|
@ -28,8 +28,7 @@ certain kinds of LAMMPS simulations.
|
|||
4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#4_15
|
||||
4.16 "Thermostatting, barostatting and computing temperature"_#4_16
|
||||
4.17 "Walls"_#4_17
|
||||
4.18 "Elastic constants"_#4_18
|
||||
4.19 "Computing free energies from thermodyanmic integration"_#4_19 :all(b)
|
||||
4.18 "Elastic constants"_#4_18 :all(b)
|
||||
|
||||
The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in "this section"_Section_example.html also show how to
|
||||
|
|
@ -164,19 +163,18 @@ the same as in 3d.
|
|||
|
||||
:line
|
||||
|
||||
4.3 CHARMM and AMBER force fields :link(4_3),h4
|
||||
4.3 CHARMM, AMBER, and DREIDING force fields :link(4_3),h4
|
||||
|
||||
There are many different ways to compute forces in the "CHARMM"_charmm
|
||||
and "AMBER"_amber molecular dynamics codes, only some of which are
|
||||
available as options in LAMMPS. A force field has 2 parts: the
|
||||
formulas that define it and the coefficients used for a particular
|
||||
system. Here we only discuss formulas implemented in LAMMPS. Setting
|
||||
A force field has 2 parts: the formulas that define it and the
|
||||
coefficients used for a particular system. Here we only discuss
|
||||
formulas implemented in LAMMPS that correspond to formulas commonly
|
||||
used in the CHARMM, AMBER, and DREIDING force fields. Setting
|
||||
coefficients is done in the input data file via the
|
||||
"read_data"_read_data.html command or in the input script with
|
||||
commands like "pair_coeff"_pair_coeff.html or
|
||||
"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html for
|
||||
additional tools that can use CHARMM or AMBER to assign force field
|
||||
coefficients and convert their output into LAMMPS input.
|
||||
"bond_coeff"_bond_coeff.html. See "this section"_Section_tools.html
|
||||
for additional tools that can use CHARMM or AMBER to assign force
|
||||
field coefficients and convert their output into LAMMPS input.
|
||||
|
||||
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
|
||||
field. See "(Cornell)"_#Cornell for a description of the AMBER force
|
||||
|
|
@ -189,16 +187,56 @@ These style choices compute force field formulas that are consistent
|
|||
with common options in CHARMM or AMBER. See each command's
|
||||
documentation for the formula it computes.
|
||||
|
||||
"bond_style"_bond_style.html harmonic
|
||||
"angle_style"_angle_style.html charmm
|
||||
"dihedral_style"_dihedral_style.html charmm
|
||||
"pair_style"_pair_style.html lj/charmm/coul/charmm
|
||||
"pair_style"_pair_style.html lj/charmm/coul/charmm/implicit
|
||||
"pair_style"_pair_style.html lj/charmm/coul/long :ul
|
||||
"bond_style"_bond_harmonic.html harmonic
|
||||
"angle_style"_angle_charmm.html charmm
|
||||
"dihedral_style"_dihedral_charmm.html charmm
|
||||
"pair_style"_pair_charmm.html lj/charmm/coul/charmm
|
||||
"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
|
||||
"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
|
||||
|
||||
"special_bonds"_special_bonds.html charmm
|
||||
"special_bonds"_special_bonds.html amber :ul
|
||||
|
||||
DREIDING is a generic force field developed by the "Goddard
|
||||
group"_http://www.wag.caltech.edu at Caltech and is useful for
|
||||
predicting structures and dynamics of organic, biological and
|
||||
main-group inorganic molecules. The philosophy in DREIDING is to use
|
||||
general force constants and geometry parameters based on simple
|
||||
hybridization considerations, rather than individual force constants
|
||||
and geometric parameters that depend on the particular combinations of
|
||||
atoms involved in the bond, angle, or torsion terms. DREIDING has an
|
||||
"explicit hydrogen bond term"_pair_hbond_dreiding.html to describe
|
||||
interactions involving a hydrogen atom (H___A) on very electronegative
|
||||
atoms (N, O, F).
|
||||
|
||||
See "(Mayo)"_#Mayo for a description of the DREIDING force field
|
||||
|
||||
These style choices compute force field formulas that are consistent
|
||||
with the DREIDING force field. See each command's
|
||||
documentation for the formula it computes.
|
||||
|
||||
"bond_style"_bond_harmonic.html harmonic
|
||||
"bond_style"_bond_morse.html morse :ul
|
||||
|
||||
"angle_style"_angle_harmonic.html harmonic
|
||||
"angle_style"_angle_cosine.html cosine
|
||||
"angle_style"_angle_cosine_periodic.html cosine/periodic :ul
|
||||
|
||||
"dihedral_style"_dihedral_charmm.html charmm
|
||||
"improper_style"_improper_umbrella.html umbrella :ul
|
||||
|
||||
"pair_style"_pair_buck.html buck
|
||||
"pair_style"_pair_buck.html buck/coul/cut
|
||||
"pair_style"_pair_buck.html buck/coul/long
|
||||
"pair_style"_pair_lj.html lj/cut
|
||||
"pair_style"_pair_lj.html lj/cut/coul/cut
|
||||
"pair_style"_pair_lj.html lj/cut/coul/long :ul
|
||||
|
||||
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/lj
|
||||
"pair_style"_pair_hbond_dreiding.html hbond/dreiding/morse :ul
|
||||
|
||||
"special_bonds"_special_bonds.html dreiding :ul
|
||||
|
||||
:line
|
||||
|
||||
4.4 Running multiple simulations from one input script :link(4_4),h4
|
||||
|
|
@ -1596,72 +1634,6 @@ tensor. Another approach is to sample the triclinic cell fluctuations
|
|||
that occur in an NPT simulation. This method can also be slow to
|
||||
converge and requires careful post-processing "(Shinoda)"_#Shinoda
|
||||
|
||||
:line
|
||||
|
||||
4.19 Computing free energies from thermodynamic integration :link(4_19),h4
|
||||
|
||||
Thermodynamic integration is a widely used method to compute free
|
||||
energies from atomistic simulations. LAMMPS can be used to run
|
||||
thermodynamic integration calculations using the methods discussed in
|
||||
this section and the "fix adapt"_fix_adapt.html command. Currently,
|
||||
it is capable of the transformations essential for computing melting
|
||||
points using the pseudo-supercritical path method developed by "Eike
|
||||
and Maginn"_#Eike_Maginn.
|
||||
|
||||
See the examples/TI directory for more information and sample files
|
||||
that compute a melting point using the techniques described in this
|
||||
section. That directory has its own README file. See also the paper
|
||||
by "Jayaraman"_#Jayaraman for an example of using this implementation
|
||||
of thermodynamic integration in LAMMPS to compute melting points of
|
||||
alkali nitrate salts, using the steps outlined here.
|
||||
|
||||
In this method, three intermediate "pseudo-supercritical" states are
|
||||
accessed in the transformation between the liquid and solid
|
||||
phases. These pseudo-states are a weak liquid, a dense weak liquid,
|
||||
and an ordered weak phase. The transformation between the liquid and
|
||||
solid states can also be driven uisng the "fix adapt"_fix_adapt.html
|
||||
command.
|
||||
|
||||
For the transformation from the liquid to the weak phase, the
|
||||
intermolecular interactions need to be weakened. Appropriate scale
|
||||
factors, computed by variables you define, and applied to pair styles
|
||||
by "fix adapt"_fix_adapt.html, can be used to do this, as in the
|
||||
example scripts. The "compute ti"_compute_ti.html command can
|
||||
accumulate the value of dU/d{lambda}. See "Jayaraman and
|
||||
Maginn"_#Jayaraman_Maginn for more information about calculating a
|
||||
free energy from dU/d{lambda}.
|
||||
|
||||
IMPORTANT NOTE: The pair styles that fix adapt can scale on-the-fly
|
||||
are listed on the "fix adapt"_fix_adapt doc page. interaction scaling
|
||||
is desired. If a pair style is not on that list, it is generally
|
||||
quite easy to add an extract() method to the pair style, to enable fix
|
||||
adapt to rescale it.
|
||||
|
||||
Step 2 is the transformation of the simulation box density from the
|
||||
liquid phase to that of the equilibrated crystal. The parameters for
|
||||
box1 and box2 should be obtained from equilibrated NPT simulations of
|
||||
the liquid and crystal phases and used in a "fix
|
||||
deform"_fix_deform.html command to change the box size and/or shape.
|
||||
It also advisable to use "fix adapt"_fix_adapt.html on the pair styles
|
||||
to prevent overlaps which may occur during the box transformation.
|
||||
|
||||
In step 3, the dense, weak system is transformed to an ordered state,
|
||||
which has the same ordering as in the equilibrated crystal. Ordering
|
||||
is achieved by introducing an attractive potential between atoms and
|
||||
lattice sites. These lattice sites can be calculated as the mean
|
||||
positions of the atoms in an equilibrium simulation of the
|
||||
crystal. The "pair/gauss"_pair_gauss.html command can be used to
|
||||
introduce an attractive Gaussian potential between the atoms and their
|
||||
corresponding lattice sites. The prefactor of the Gaussian pair
|
||||
potential can be scaled by "fix adapt"_fix_adapt.html to turn on the
|
||||
attractions. Again, the quantity dU/d{lambda} can be tracked via the
|
||||
"compute ti"_compute_ti.html command.
|
||||
|
||||
Step 4 is the transformation of the ordered state to the final
|
||||
crystal. In this step, the intermolecular interactions are scaled
|
||||
back to full strength, while the Gaussian tethers are removed, all via
|
||||
"fix adapt"_fix_adapt.html.
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
|
|
@ -1681,6 +1653,10 @@ J Chem Phys, 120, 9665 (2004).
|
|||
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
|
||||
:link(Mayo)
|
||||
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
|
||||
:link(Jorgensen)
|
||||
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
|
||||
Phys, 79, 926 (1983).
|
||||
|
|
@ -1690,15 +1666,3 @@ Phys, 79, 926 (1983).
|
|||
|
||||
:link(Shinoda)
|
||||
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
|
||||
:link(Eike_Maginn)
|
||||
[(Eike and Maginn)] Eike and Maginn, J Chem Phys, 124,
|
||||
164503 (2006).
|
||||
|
||||
:link(Jayaraman_Maginn)
|
||||
[(Jayaraman and Maginn)] Jayaraman and Maginn, Journal of Chemical Physics,
|
||||
127, 214504 (2007).
|
||||
|
||||
:link(Jayaraman)
|
||||
[(Jayaraman)] Jayaraman, Thompson, von Lilienfeld and Maginn, Industrial
|
||||
and Engineering Chemistry Research, 49, 559-571 (2010).
|
||||
|
|
|
|||
|
|
@ -13,15 +13,17 @@
|
|||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>compute ID group-ID pair pstyle
|
||||
<PRE>compute ID group-ID pair pstyle evalue
|
||||
</PRE>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>pair = style name of this compute command
|
||||
<LI>pstyle = style name of a pair style that calculates additional values
|
||||
<LI>evalue = <I>epair</I> or <I>evdwl</I> or <I>evoul</I> or blank (optional setting)
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute 1 all pair gauss
|
||||
compute 1 all pair lj/cut/coul/cut ecoul
|
||||
compute 1 all pair reax
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
|
|
@ -31,32 +33,44 @@ pair style, sums them across processors, and makes them accessible for
|
|||
output or further processing by other commands. The group specified
|
||||
for this command is ignored.
|
||||
</P>
|
||||
<P>The specified <I>pstyle</I> must be a pair style that produces additional
|
||||
values. If a <A HREF = "pair_hybrid.html">hybrid pair style</A> is used, then
|
||||
<I>pstyle</I> should be the name of a sub-style.
|
||||
<P>The specified <I>pstyle</I> must be a pair style used in your simulation
|
||||
either by itself or as a sub-style in a <A HREF = "pair_hybrid.html">pair_style hybrid or
|
||||
hybrid/overlay</A> command.
|
||||
</P>
|
||||
<P>All pair styles tally a potential energy, which is accessed by the
|
||||
<A HREF = "compute_pe.html">compute pe</A> and <A HREF = "compute_pe_atom.html">compute
|
||||
pe/atom</A> commands. Some pair styles tally one or
|
||||
more additional values, such as a breakdown of the total pair
|
||||
potential energy into sub-categories. See the doc page for
|
||||
<P>The <I>evalue</I> setting is optional; it may be left off the command. All
|
||||
pair styles tally a potential energy <I>epair</I> which may be broken into
|
||||
two parts: <I>evdwl</I> and <I>ecoul</I> such that <I>epair</I> = <I>evdwl</I> + <I>evoul</I>.
|
||||
If the pair style calculates Coulombic interactions, their energy will
|
||||
be tallied in <I>ecoul</I>. Everything else (whether it is a Lennard-Jones
|
||||
style van der Waals interaction or not) is tallied in <I>evdwl</I>. If
|
||||
<I>evalue</I> is specified as <I>epair</I> or left out, then <I>epair</I> is stored
|
||||
as a global scalar by this compute. This is useful when using
|
||||
<A HREF = "pair_hybrid.html">pair_style hybrid</A> if you want to know the portion
|
||||
of the total energy contributed by one sub-style. If <I>evalue</I> is
|
||||
specfied as <I>evdwl</I> or <I>ecoul</I>, then just that portion of the energy
|
||||
is stored as a global scalar.
|
||||
</P>
|
||||
<P>Some pair styles tally additional quantities, e.g. a breakdown of
|
||||
potential energy into a dozen or so components is tallied by the
|
||||
<A HREF = "pair_reax.html">pair_style reax</A> commmand. These values (1 or more)
|
||||
are stored as a global vector by this compute. See the doc page for
|
||||
<A HREF = "pair_style.html">individual pair styles</A> for info on these values.
|
||||
</P>
|
||||
<P>The compute pair command lets you access this data as a global vector
|
||||
of values and then use other <A HREF = "Section_howto.html#4_15">output options</A>
|
||||
that work with <A HREF = "compute.html">compute commands</A> to see or use the
|
||||
values.
|
||||
</P>
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
<P>This compute calculates a global vector of length >= 1, as determined
|
||||
by the pair style. These values can be used by any command that uses
|
||||
global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
|
||||
section</A> for an overview of LAMMPS output
|
||||
options.
|
||||
<P>This compute calculates a global scalar which is <I>epair</I> or <I>evdwl</I> or
|
||||
<I>evoul</I>. If the pair style supports it, it also calculates a global
|
||||
vector of length >= 1, as determined by the pair style. These values
|
||||
can be used by any command that uses global scalar or vector values
|
||||
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
|
||||
for an overview of LAMMPS output options.
|
||||
</P>
|
||||
<P>The vector values calculated by this compute are "extensive". They
|
||||
are in whatever units the pair style produces.
|
||||
<P>The scalar and vector values calculated by this compute are
|
||||
"extensive".
|
||||
</P>
|
||||
<P>The scalar value will be in energy <A HREF = "units.html">units</A>. The vector
|
||||
values will typically also be in energy <A HREF = "units.html">units</A>, but
|
||||
see the doc page for the pair style for details.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
|
|
@ -64,6 +78,8 @@ are in whatever units the pair style produces.
|
|||
</P>
|
||||
<P><A HREF = "compute_pe.html">compute pe</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The default for <I>evalue</I> is <I>epair</I>.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -10,15 +10,17 @@ compute pair command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID pair pstyle :pre
|
||||
compute ID group-ID pair pstyle evalue :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
pair = style name of this compute command
|
||||
pstyle = style name of a pair style that calculates additional values :ul
|
||||
pstyle = style name of a pair style that calculates additional values
|
||||
evalue = {epair} or {evdwl} or {evoul} or blank (optional setting) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 all pair gauss
|
||||
compute 1 all pair lj/cut/coul/cut ecoul
|
||||
compute 1 all pair reax :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -28,32 +30,44 @@ pair style, sums them across processors, and makes them accessible for
|
|||
output or further processing by other commands. The group specified
|
||||
for this command is ignored.
|
||||
|
||||
The specified {pstyle} must be a pair style that produces additional
|
||||
values. If a "hybrid pair style"_pair_hybrid.html is used, then
|
||||
{pstyle} should be the name of a sub-style.
|
||||
The specified {pstyle} must be a pair style used in your simulation
|
||||
either by itself or as a sub-style in a "pair_style hybrid or
|
||||
hybrid/overlay"_pair_hybrid.html command.
|
||||
|
||||
All pair styles tally a potential energy, which is accessed by the
|
||||
"compute pe"_compute_pe.html and "compute
|
||||
pe/atom"_compute_pe_atom.html commands. Some pair styles tally one or
|
||||
more additional values, such as a breakdown of the total pair
|
||||
potential energy into sub-categories. See the doc page for
|
||||
The {evalue} setting is optional; it may be left off the command. All
|
||||
pair styles tally a potential energy {epair} which may be broken into
|
||||
two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {evoul}.
|
||||
If the pair style calculates Coulombic interactions, their energy will
|
||||
be tallied in {ecoul}. Everything else (whether it is a Lennard-Jones
|
||||
style van der Waals interaction or not) is tallied in {evdwl}. If
|
||||
{evalue} is specified as {epair} or left out, then {epair} is stored
|
||||
as a global scalar by this compute. This is useful when using
|
||||
"pair_style hybrid"_pair_hybrid.html if you want to know the portion
|
||||
of the total energy contributed by one sub-style. If {evalue} is
|
||||
specfied as {evdwl} or {ecoul}, then just that portion of the energy
|
||||
is stored as a global scalar.
|
||||
|
||||
Some pair styles tally additional quantities, e.g. a breakdown of
|
||||
potential energy into a dozen or so components is tallied by the
|
||||
"pair_style reax"_pair_reax.html commmand. These values (1 or more)
|
||||
are stored as a global vector by this compute. See the doc page for
|
||||
"individual pair styles"_pair_style.html for info on these values.
|
||||
|
||||
The compute pair command lets you access this data as a global vector
|
||||
of values and then use other "output options"_Section_howto.html#4_15
|
||||
that work with "compute commands"_compute.html to see or use the
|
||||
values.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global vector of length >= 1, as determined
|
||||
by the pair style. These values can be used by any command that uses
|
||||
global vector values from a compute as input. See "this
|
||||
section"_Section_howto.html#4_15 for an overview of LAMMPS output
|
||||
options.
|
||||
This compute calculates a global scalar which is {epair} or {evdwl} or
|
||||
{evoul}. If the pair style supports it, it also calculates a global
|
||||
vector of length >= 1, as determined by the pair style. These values
|
||||
can be used by any command that uses global scalar or vector values
|
||||
from a compute as input. See "this section"_Section_howto.html#4_15
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive". They
|
||||
are in whatever units the pair style produces.
|
||||
The scalar and vector values calculated by this compute are
|
||||
"extensive".
|
||||
|
||||
The scalar value will be in energy "units"_units.html. The vector
|
||||
values will typically also be in energy "units"_units.html, but
|
||||
see the doc page for the pair style for details.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
@ -61,4 +75,6 @@ are in whatever units the pair style produces.
|
|||
|
||||
"compute pe"_compute_pe.html
|
||||
|
||||
[Default:] none
|
||||
[Default:]
|
||||
|
||||
The default for {evalue} is {epair}.
|
||||
|
|
|
|||
|
|
@ -17,10 +17,11 @@
|
|||
</PRE>
|
||||
<UL><LI>one or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
|
||||
<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>dreiding</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
|
||||
|
||||
<PRE> <I>amber</I> values = none
|
||||
<I>charmm</I> values = none
|
||||
<I>dreiding</I> values = none
|
||||
<I>fene</I> values = none
|
||||
<I>lj/coul</I> values = w1,w2,w3
|
||||
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
|
||||
|
|
@ -80,7 +81,8 @@ details.
|
|||
<P>The <I>amber</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
|
||||
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
|
||||
is the default for a commonly used version of the AMBER force field,
|
||||
where the last value is really 5/6.
|
||||
where the last value is really 5/6. See <A HREF = "#Cornell">(Cornell)</A> for a
|
||||
description of the AMBER force field.
|
||||
</P>
|
||||
<P>The <I>charmm</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
|
||||
LJ and Coulombic interactions, which is the default for a commonly
|
||||
|
|
@ -89,11 +91,17 @@ used version of the CHARMM force field. Note that in pair styles
|
|||
are defined explicitly, and these pairwise contributions are computed
|
||||
as part of the charmm dihedral style - see the
|
||||
<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
|
||||
commands for more information.
|
||||
commands for more information. See <A HREF = "#MacKerell">(MacKerell)</A> for a
|
||||
description of the CHARMM force field.
|
||||
</P>
|
||||
<P>The <I>dreiding</I> keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
|
||||
LJ and Coulombic interactions, which is the default for the Dreiding
|
||||
force field, as discussed in <A HREF = "#Mayo">(Mayo)</A>.
|
||||
</P>
|
||||
<P>The <I>fene</I> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
|
||||
LJ and Coulombic interactions, which is consistent with a
|
||||
coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>.
|
||||
coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>. See
|
||||
<A HREF = "#Kremer">(Kremer)</A> for a description of FENE bonds.
|
||||
</P>
|
||||
<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
|
||||
be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
|
||||
|
|
@ -150,4 +158,25 @@ you do not do this, you may get an error when bonds are added.
|
|||
<P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
|
||||
angle = no, dihedral = no, and extra = 0.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Cornell"></A>
|
||||
|
||||
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
||||
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
||||
</P>
|
||||
<A NAME = "Kremer"></A>
|
||||
|
||||
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
</P>
|
||||
<A NAME = "MacKerell"></A>
|
||||
|
||||
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
</P>
|
||||
<A NAME = "Mayo"></A>
|
||||
|
||||
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -13,9 +13,10 @@ special_bonds command :h3
|
|||
special_bonds keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be appended :ulb,l
|
||||
keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
|
||||
keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
|
||||
{amber} values = none
|
||||
{charmm} values = none
|
||||
{dreiding} values = none
|
||||
{fene} values = none
|
||||
{lj/coul} values = w1,w2,w3
|
||||
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
|
||||
|
|
@ -74,7 +75,8 @@ details.
|
|||
The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
|
||||
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
|
||||
is the default for a commonly used version of the AMBER force field,
|
||||
where the last value is really 5/6.
|
||||
where the last value is really 5/6. See "(Cornell)"_#Cornell for a
|
||||
description of the AMBER force field.
|
||||
|
||||
The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
|
||||
LJ and Coulombic interactions, which is the default for a commonly
|
||||
|
|
@ -83,11 +85,17 @@ used version of the CHARMM force field. Note that in pair styles
|
|||
are defined explicitly, and these pairwise contributions are computed
|
||||
as part of the charmm dihedral style - see the
|
||||
"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
|
||||
commands for more information.
|
||||
commands for more information. See "(MacKerell)"_#MacKerell for a
|
||||
description of the CHARMM force field.
|
||||
|
||||
The {dreiding} keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
|
||||
LJ and Coulombic interactions, which is the default for the Dreiding
|
||||
force field, as discussed in "(Mayo)"_#Mayo.
|
||||
|
||||
The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
|
||||
LJ and Coulombic interactions, which is consistent with a
|
||||
coarse-grained polymer model with "FENE bonds"_bond_fene.html.
|
||||
coarse-grained polymer model with "FENE bonds"_bond_fene.html. See
|
||||
"(Kremer)"_#Kremer for a description of FENE bonds.
|
||||
|
||||
The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
|
||||
be set explicitly. The {lj/coul} keyword sets both the LJ and
|
||||
|
|
@ -143,3 +151,21 @@ you do not do this, you may get an error when bonds are added.
|
|||
|
||||
All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
|
||||
angle = no, dihedral = no, and extra = 0.
|
||||
|
||||
:line
|
||||
|
||||
:link(Cornell)
|
||||
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
||||
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
||||
|
||||
:link(Kremer)
|
||||
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
|
||||
:link(MacKerell)
|
||||
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||
|
||||
:link(Mayo)
|
||||
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
||||
(1990).
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue