From b5a528fbacd66b8f932039a2573c17ab1f2ec33b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 9 Aug 2010 14:53:25 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4472 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_howto.html | 31 ++++++++++++++++++++++++++----- doc/Section_howto.txt | 30 +++++++++++++++++++++++++----- 2 files changed, 51 insertions(+), 10 deletions(-) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 25886e8294..09f29c6315 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -421,6 +421,9 @@ r0 of OH bond = 0.9572

K of HOH angle = 55
theta of HOH angle = 104.52

+

Wikipedia also has a nice article on water +models. +

4.8 TIP4P water model @@ -477,6 +480,9 @@ theta of HOH angle = 104.52
LJ sigma of O-O = 3.16435
LJ epsilon, sigma of OH, HH = 0.0

+

Wikipedia also has a nice article on water +models. +

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.

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
@@ -505,13 +510,24 @@ LJ epsilon, sigma of OH, HH = 0.0

r0 of OH bond = 1.0
theta of HOH angle = 109.47

-

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

+

See the (Berendsen) reference for more details on both +the SPC and SPC/E models. +

+

Wikipedia also has a nice article on water +models. +

4.10 Coupling LAMMPS to other codes @@ -1492,6 +1508,11 @@ converge and requires careful post-processing (Shinoda)
+ + +

(Berendsen) Berendsen, Grigera, Straatsma, J Phys Chem, 91, +6269-6271 (1987). +

(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 3597c9747d..3791eaf01c 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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).