[gmx-users] enegry minimisation

[Justin A. Lemkul]

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 /<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.
> 
>     -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

========================================