Re: [AMBER] turning off solute-solvent interactions

From: Brian Radak <radak004.umn.edu>
Date: Mon, 5 Mar 2012 17:01:27 -0500

Hi Andy,

I believe there was some discussion of this on the mailing list recently.
I don't know what the ultimate conclusion was, but I think the answer to
your final question ("is there a simple solution?") is "not really" or
maybe more optimistically "that depends on what you mean by simple."

A really quick search on Google gave me these threads:

http://archive.ambermd.org/201108/0046.html

http://archive.ambermd.org/201112/0128.htm<http://archive.ambermd.org/201112/0128.html>

Hopefully someone else can be more helpful.

Regards,
Brian

On Mon, Mar 5, 2012 at 4:22 PM, Andy Ballard <ballard.andy.gmail.com> wrote:

> Hi,
>
> I'd like to set up a simulation of a solute in explicit solvent in which
> the solute-solvent interactions can be selectively turned off. (i.e. The
> force acting on a particular solute (solvent) atom is determined only by
> the the other solute (solvent) atoms, and not the solvent (solute) atoms; )
>
> The question I have is how to implement this in the topology file. I
> understand I could turn off the solute-solvent Lennard Jones interactions
> by editing the relevant ACOEF and BCOEF values in the prmtop file (is there
> anything else that would need to be modified?), but I'm not sure how to
> turn off the coulomb interactions.
>
> Can anyone see a simple solution to this?
>
> Thanks in advance for any help.
>
> Andy
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
08854-8066
 radak004.umn.edu                                 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 05 2012 - 14:30:03 PST
Custom Search