[gmx-users] enegry minimisation

sonali dhindwal 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.
nstcomm             =1
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
; 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.

Sonali Dhindwal

--- 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
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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