Sai Pooja wrote:
When using the charmm forcefield, the following is the case:
1. ffnonbonded.itp - has listed paramters for tip3p (and other water
models) OWT3 and HWT3
2. ffbonded.itp - does not have paramters for OWT3 and HWT3
Does this mean:
1. nonbonded parameters for tip3p are read from ffnonbonded.itp for ALL
nonbonded interactions OR
for water-water interactions are read from tip3p.itp file and for
protein-water are read from ffnonbonded.itp?
Nonbonded interactions are applied uniformly, unless they are modified in a
specific [nonbond_params] directive. Isn't this something we've worked through
before?
http://lists.gromacs.org/pipermail/gmx-users/2010-October/055332.html
2.bonded paramters for tip3p are read from tip3p.itp file?
Bonded parameters for water models are really only relevant if using a flexible
model (which you shouldn't). Otherwise, the SETTLE algorithm simply fixes the
geometry. This is all determined by the #ifdef FLEXIBLE statement in, for
instance, tip3p.itp.
-Justin
Pooja
--
Quaerendo Invenietis-Seek and you shall discover.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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