[gmx-users] tip3p itp file parameters

[Justin A. Lemkul]

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.
> 

-- 
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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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