[gmx-users] tip3p itp file parameters

[Mark Abraham]

On 5/11/2010 6:36 AM, Sai Pooja wrote:
> Thanks Justin. I was just making sure that I was modifying the 
> relevant files.

You can verify things for yourself by making a .tpr, making the change, 
making the new .tpr and then using gmxcheck to compare the two.

Mark

> On Thu, Nov 4, 2010 at 2:17 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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 <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
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>
> -- 
> Quaerendo Invenietis-Seek and you shall discover.

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