[gmx-users] GROMACS parameterization

[Berk Hess]

Ah, I can make some more advertisement for my own work.
Have a look at this paper:
http://dx.doi.org/10.1021/jp0641029

Berk

> Date: Fri, 31 Jul 2009 20:40:31 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] GROMACS parameterization
> 
> 
> 
> rams rams wrote:
> > Hello users,
> > I have a question about the Gromacs parameterization. 
> > By using which water model (SPC / SPC/E / TIP3P etc) and their variants, 
> > the protein force field parameters in GROMACS were optimized ? 
> 
> This information can be found in the primary literature for each force field. 
> Further comparative studies can also be found that compare different water 
> models with different force fields.
> 
> -Justin
> 
> > Since a few of the properties of proteins depends upon the water models 
> > we employ (for instance, SPC water model over estimates the 
> > diffusion properties of the proteins by a factor of approx. 2). it is 
> > necessary to know which water model needs to be used in the simulation.
> > Thanks in advance.
> > Ram. 
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
What can you do with the new Windows Live? Find out
http://www.microsoft.com/windows/windowslive/default.aspx
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090803/ba426479/attachment.html>