[gmx-users] electrostatic interactions
abdullah_renk_ahmed at hotmail.com
Mon May 3 18:30:40 CEST 2010
Thank you for your reply,
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
define = -DPOSRES
integrator = steep
nsteps = 100
Energy minimizing stuff
emtol = 20
nstcgsteep = 10
nstcomm = 1
rlist = 1
rcoulomb = 1.0
Tcoupl = no
Pcoupl = 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.
> > 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
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