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@ -17,7 +17,7 @@
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</PRE>
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<UL><LI>one or more keyword/value pairs may be appended
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<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>dihedral</I> or <I>extra</I>
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<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>
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<PRE> <I>amber</I> values = none
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<I>charmm</I> values = none
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@ -28,6 +28,7 @@
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
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<I>coul</I> values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
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<I>angle</I> value = <I>yes</I> or <I>no</I>
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<I>dihedral</I> value = <I>yes</I> or <I>no</I>
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<I>extra</I> value = N
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N = number of extra 1-2,1-3,1-4 interactions to save space for
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@ -39,7 +40,7 @@
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<PRE>special_bonds amber
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special_bonds charmm
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special_bonds fene dihedral no
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special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
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special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
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special_bonds lj/coul 0 1 1 extra 2
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</PRE>
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@ -69,8 +70,8 @@ apply to is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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</P>
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<P>The two exceptions to this rule are (a) if the <I>dihedral</I> keyword is
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set to <I>yes</I> (see below), or (b) if the
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<P>The two exceptions to this rule are (a) if the <I>angle</I> or <I>dihedral</I>
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keywords are set to <I>yes</I> (see below), or (b) if the
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<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
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@ -101,6 +102,20 @@ keywords only set either the LJ or Coulombic coefficients. Use both
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of them if you wish to set the LJ coefficients to different values
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than the Coulombic coefficients.
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</P>
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<P>The <I>angle</I> keyword allows the 1-3 weighting factor to be ignored for
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individual atom pairs if they are not listed as the first and last
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atoms in any angle defined in the simulation. For example, imagine
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the 1-3 weighting factor is set to 0.5 and you have a linear molecule
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with 4 atoms and bonds as follows: 1-2-3-4. If your data file defines
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1-2-3 as an angle, but does not define 2-3-4 as an angle, then the
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pairwise interaction between atoms 1 and 3 will always be weighted by
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0.5, but different force fields use different rules for weighting the
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pairwise interaction between atoms 2 and 4. If the <I>angle</I> keyword is
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specified as <I>yes</I>, then the pairwise interaction between atoms 2 and
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4 will be unaffected (full weighting of 1.0). If the <I>angle</I> keyword
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is specified as <I>no</I> which is the default, then the 2,4 interaction
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will also be weighted by 0.5.
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</P>
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<P>The <I>dihedral</I> keyword allows the 1-4 weighting factor to be ignored
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for individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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@ -132,6 +147,6 @@ you do not do this, you may get an error when bonds are added.
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<P><B>Default:</B>
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</P>
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<P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
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dihedral = no, and extra = 0.
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angle = no, dihedral = no, and extra = 0.
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</P>
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</HTML>
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@ -13,7 +13,7 @@ special_bonds command :h3
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special_bonds keyword values ... :pre
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one or more keyword/value pairs may be appended :ulb,l
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keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihedral} or {extra} :l
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keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
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{amber} values = none
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{charmm} values = none
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{fene} values = none
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@ -23,6 +23,7 @@ keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihed
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
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{coul} values = w1,w2,w3
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w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
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{angle} value = {yes} or {no}
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{dihedral} value = {yes} or {no}
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{extra} value = N
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N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
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@ -33,7 +34,7 @@ Examples:
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special_bonds amber
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special_bonds charmm
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special_bonds fene dihedral no
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special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
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special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
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special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
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special_bonds lj/coul 0 1 1 extra 2 :pre
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@ -63,8 +64,8 @@ apply to is the same whether angle and dihedral potentials are
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computed or not, and remains the same even if bonds are constrained,
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or turned off, or removed during a simulation.
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The two exceptions to this rule are (a) if the {dihedral} keyword is
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set to {yes} (see below), or (b) if the
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The two exceptions to this rule are (a) if the {angle} or {dihedral}
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keywords are set to {yes} (see below), or (b) if the
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"delete_bonds"_delete_bonds.html command is used with the {special}
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option that recomputes the 1-2,1-3,1-4 topologies after bonds are
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deleted; see the "delete_bonds"_delete_bonds.html command for more
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@ -95,6 +96,20 @@ keywords only set either the LJ or Coulombic coefficients. Use both
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of them if you wish to set the LJ coefficients to different values
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than the Coulombic coefficients.
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The {angle} keyword allows the 1-3 weighting factor to be ignored for
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individual atom pairs if they are not listed as the first and last
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atoms in any angle defined in the simulation. For example, imagine
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the 1-3 weighting factor is set to 0.5 and you have a linear molecule
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with 4 atoms and bonds as follows: 1-2-3-4. If your data file defines
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1-2-3 as an angle, but does not define 2-3-4 as an angle, then the
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pairwise interaction between atoms 1 and 3 will always be weighted by
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0.5, but different force fields use different rules for weighting the
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pairwise interaction between atoms 2 and 4. If the {angle} keyword is
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specified as {yes}, then the pairwise interaction between atoms 2 and
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4 will be unaffected (full weighting of 1.0). If the {angle} keyword
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is specified as {no} which is the default, then the 2,4 interaction
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will also be weighted by 0.5.
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The {dihedral} keyword allows the 1-4 weighting factor to be ignored
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for individual atom pairs if they are not listed as the first and last
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atoms in any dihedral defined in the simulation. For example, imagine
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@ -126,4 +141,4 @@ you do not do this, you may get an error when bonds are added.
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[Default:]
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All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
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dihedral = no, and extra = 0.
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angle = no, dihedral = no, and extra = 0.
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