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
> can’t 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 ======================================================================
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:00 CST