[gmx-users] electrostatic interactions

[abdullah ahmed]

Thank you for your reply, 

Settings: 
I am using the procedure
 outline by the "speptide" tutorial (i.e. pdb2gmx, followed by editconf,
 genbox, grompp, and mdrun). The ".mdp" file I've used is as follows: 

;   
 User spoel (236)
;    Wed Nov  3 17:12:44 1993
;    Input file
;
cpp                
 =  /usr/bin/cpp
define              =  -DPOSRES 
constraints        
 =  none
integrator          =  steep
nsteps              =  100
;
;   
 Energy minimizing stuff
;
emtol               =  20
emstep             
 =  0.01

nstcgsteep          =  10
nstcomm             =  1
ns_type            
 =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw               
 =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel            
 =  no
coulombtype         = PME

Force field: Encad all atom 
force field, using full sovent charges.

Local geometry is 
identical with the exception of the second charged residue, which is 
replaced by Leucine in one structure.  

> Date: Mon, 3 May 2010 12:11:12 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] electrostatic interactions
> 
> 
> 
> 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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> 
> -- 
> ========================================
> 
> 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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