sonali dhindwal wrote:
Thanks Justin for your reply.
Yes I have included solvent in the protein using genbox.
Then you should do energy minimization after constructing the system.
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.
nstcomm =1
I don't know if this matters or not, but I think your parameters and values
should be separated from the '=' by whitespace. I also don't know if that will
have any effect on your unstable system (see below), but do check to make sure
that all of your settings have been interpreted correctly. Confirm your input
settings with the mdout.mdp file produced by grompp.
nstxout = 500 ; output coordinates every 1.0 ps
nstvout =0
nstfout =0
nstlist = 5
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 1.4
fourierspacing = 0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =6
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
This thermostat setup is certainly incorrect. You should not couple all the
components of your system to separate thermostats. See here:
http://www.gromacs.org/Documentation/Terminology/Thermostats
You have a fairly complicated system. Are some of these species small
molecules? If so, how did you derive their parameters? Have you demonstrated
that these parameters are accurate? Which structure is falling apart, and how
are you making that assessment?
-Justin
; 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.
Thanks
--
Sonali Dhindwal
--- On *Wed, 19/5/10, Justin A. Lemkul /<jalem...@vt.edu>/* wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] enegry minimisation
To: "Discussion list for GROMACS users" <gmx-users@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.
-Justin
> Thanks and regards
> ^
>
> --
> Sonali Dhindwal
>
>
-- ========================================
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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--
========================================
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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