[gmx-users] electrostatic interactions

Justin A. Lemkul jalemkul at vt.edu
Mon May 3 18:11:12 CEST 2010

abdullah ahmed wrote:
> Hello everyone,
> I have just started using GROMACS, and apolise if my question is naive.
> Basically, I'd like to ask if anyone has some suggestions regarding the 
> settings I should use for electrostatic interactions?

Well, you haven't shown us what settings you're using or what force field you're 
using, so it's impossible to make any specific recommendation.  Your cutoffs and 
type of long-range electrostatics method will be largely dictated by the force 
field you've chosen.  The primary literature will tell you a lot.

> I have two protein molecules similar in everyway except, one has a 
> single negative charge inside the molecule, and another has two opposite 
> charges facing each other. The opposite charges are close enough to form 
> electrostatic interactions, so would expect the coloumb energy for this 
> molecule to be less than the other after minimization/molecular 
> dynamics. However, the results show that they are almost the same.

It's hard to comment on the accuracy of these results without a lot more 
information (see above).  Other factors include the local geometry of other 
surrounding residues; if the structures are different (even subtly) you 
certainly can't make any generalizations.


> Thank you in advance for your help,
> Abdullah Ahmed
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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