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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4472 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2010-08-09 14:53:25 +00:00
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31
doc/Section_howto.html
View File

@ -421,6 +421,9 @@ r0 of OH bond = 0.9572 <BR>
<P>K of HOH angle = 55<BR>
theta of HOH angle = 104.52 <BR>
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "4_8"></A><H4>4.8 TIP4P water model
@ -477,6 +480,9 @@ theta of HOH angle = 104.52 <BR>
LJ sigma of O-O = 3.16435<BR>
LJ epsilon, sigma of OH, HH = 0.0 <BR>
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "4_9"></A><H4>4.9 SPC water model
@ -489,8 +495,7 @@ the two O-H bonds and the H-O-H angle rigid. A bond style of
used.
</P>
<P>These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model with long-range
Coulombics (Ewald or PPPM in LAMMPS).
atoms and the water molecule to run a rigid SPC model.
</P>
<P>O mass = 15.9994<BR>
H mass = 1.008 <BR>
@ -505,13 +510,24 @@ LJ epsilon, sigma of OH, HH = 0.0 <BR>
<P>r0 of OH bond = 1.0<BR>
theta of HOH angle = 109.47 <BR>
</P>
<P>To use an SPC model with a long-range Coulombic solver (Ewald or
PPPM in LAMMPS), the only parameters that change are the partial
charge assignments:
<P>Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
</P>
<P>The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:
</P>
<P>O charge = -0.8476<BR>
H charge = 0.4238 <BR>
</P>
<P>See the <A HREF = "#Berendsen">(Berendsen)</A> reference for more details on both
the SPC and SPC/E models.
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.
</P>
<HR>
<A NAME = "4_10"></A><H4>4.10 Coupling LAMMPS to other codes
@ -1492,6 +1508,11 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
<HR>
<A NAME = "Berendsen"></A>
<P><B>(Berendsen)</B> Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
</P>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,

30
doc/Section_howto.txt
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@ -417,6 +417,9 @@ r0 of OH bond = 0.9572 :all(b),p
K of HOH angle = 55
theta of HOH angle = 104.52 :all(b),p
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.8 TIP4P water model :link(4_8),h4
@ -473,6 +476,9 @@ LJ epsilon of O-O = 0.16275
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.9 SPC water model :link(4_9),h4
@ -485,8 +491,7 @@ the two O-H bonds and the H-O-H angle rigid. A bond style of
used.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid SPC model with long-range
Coulombics (Ewald or PPPM in LAMMPS).
atoms and the water molecule to run a rigid SPC model.
O mass = 15.9994
H mass = 1.008 :all(b),p
@ -501,13 +506,24 @@ LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
r0 of OH bond = 1.0
theta of HOH angle = 109.47 :all(b),p
To use an SPC model with a long-range Coulombic solver (Ewald or
PPPM in LAMMPS), the only parameters that change are the partial
charge assignments:
Note that as originally proposed, the SPC model was run with a 9
Angstrom cutoff for both LJ and Coulommbic terms. It can also be used
with long-range Coulombics (Ewald or PPPM in LAMMPS), without changing
any of the parameters above, though it becomes a different model in
that mode of usage.
The SPC/E (extended) water model is the same, except
the partial charge assignemnts change:
O charge = -0.8476
H charge = 0.4238 :all(b),p
See the "(Berendsen)"_#Berendsen reference for more details on both
the SPC and SPC/E models.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.
:line
4.10 Coupling LAMMPS to other codes :link(4_10),h4
@ -1480,6 +1496,10 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
:line
:link(Berendsen)
[(Berendsen)] Berendsen, Grigera, Straatsma, J Phys Chem, 91,
6269-6271 (1987).
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).