[gmx-users] electrostatic interactions

[Justin A. Lemkul]

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.

-Justin

> Thank you in advance for your help,
> Abdullah Ahmed
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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