[gmx-users] enegry minimisation
sonali11dhindwal at yahoo.co.in
Wed May 19 14:10:39 CEST 2010
Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.
I am pasting .mdp file which I used for MD simulation :
title = trp_drg MD
cpp = /lib/cpp ; location of cpp on SGI
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 500000 ; total 1 ns.
nstxout = 500 ; output coordinates every 1.0 ps
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in four groups
Tcoupl = berendsen
tau_t = 0.1 0.1 0.1 0.1 0.1 0.1
tc_grps = Protein SOL MG PEP E4P NA+
ref_t = 300 300 300 300 300 300
; Pressure coupling is on
Pcoupl = berendsen
pcoupltype = isotropic
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
I hope it will help you to guide me futher.
--- On Wed, 19/5/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, 19 May, 2010, 5:17 PM
sonali dhindwal wrote:
> Hello All
> This question may sound trivial to many, but as i am new to this field, please help.
> I want to ask a question regarding my previous query of distortion of protein strucutre after molecular dynamcs simulation.
Can you provide a link to your previous post, for reference?
> I have noticed that after enegry minimisation using steepest decent algorithm, using emtol of 1000 kJ mol^-1 nm^-1 .
> So is it necessary to do enegry minimisation step before MD, because this is my modeled protein, and i have already done energy minimisation using different program and after that I have done refinement also.
Have you added solvent or anything else to the protein model? If so, then the answer is yes. Solvation with a regularly-ordered lattice of solvent molecules can (and often does) lead to bad clashes with your protein structure, thus necessitating further minimization.
There are plenty of reasons why a protein structure might be unstable, most of them related to .mdp file settings, but you haven't posted those so there's no way to know if you're doing things correctly.
> Thanks and regards
> Sonali Dhindwal
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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