[gmx-users] tip3p itp file parameters

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 4 19:17:35 CET 2010

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 


> 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.


> Pooja
> -- 
> Quaerendo Invenietis-Seek and you shall discover.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list