Re: how to convert CHARMM TIP3P to traditional TIP3P

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Wed Mar 06 2013 - 09:07:55 CST

Just about anything one would want to know about the CHARMM force fields
can be found here:

http://www.charmm.org/ubbthreads/

If it's not there, you can post your question. My experience is that
people are very responsive.

Regarding NAMD, it's very easy to add other water models, you just need
to make the appropriate changes in the parameter and topology files. No
need to mess with NBFIX. That said, if you are using CHARMM for your
other molecules, you should stick with their version of TIP3P.

Regards,
     Jeff

On 3/6/2013 6:56 AM, subbarao kanchi wrote:
> Dear NAMD users,
> I searched in literature and discussion in
> NAMD Mailing List, I come to know that the water model used in CHARMM
> FF is Modified TIP3P. IN this modified TIP3P there are Non bonded
> Lennard Jones interactions in between water Hydrogen atoms but not in
> traditional TIP3P model.I Have following doubts regarding water models.
>
> 1) I know that the CHARMM FF (for bio molecules like lipid and
> proteins) parameters are developed by treating TIP3P water model But I
> canít able to find reason for introduction of Lennard Jones
> interactions in between water Hydrogen atoms.
>
> 2) If I want to run MD simulations with traditional TIP3P, Is it
> enough to avoid the Lennard Jones interactions in between water
> Hydrogen atoms by using NBFIX ?
>
> 3) I want to MD simulations of water and solid surface, which is good
> force field to use among regular TIP3P and CHARMM modified TIP3P? or
> Is it possible to used other water force field like SPC/E in NAMD ?
>
> Thanks in advance, if I get any suggestions.
>
>
> Regards,
> subbu.
>
>

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_wayne.edu
Associate Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202
http://potoff1.eng.wayne.edu
======================================================================

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