[gmx-users] problem with npt

[Justin A. Lemkul]

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
>
> I wrote yes to generate velocity. Can that be a reason for the problem? Since
> I am doing membrane simulation it is advised to do production runs in npt
> thats the only other difference.

I think what Mark was asking for was a bit more detail on how you put your
system together.  It would be helpful to know (step by step) what you did, as
that may highlight a problem.  Also, what do you define as "deformed very
much?"  Some fluctuations are to be expected, and 250 ps is a relatively short
time frame.  In some of my bilayer simulations, the lipids look quite strange
under NVT, but after a nanosecond or two or NPT they even out and behave
normally.

-Justin

> ----------------------------------------
> > Date: Sat, 15 Dec 2007 06:03:27 +1100
> > From: Mark.Abraham at anu.edu.au
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] problem with npt
> >
> > pragya chohan wrote:
> > >
> > > thanks for your help.
> > > My system ran fine for 250 ps but later the bilayer deformed very much.
> >
> > What was your system preparation protocol - i.e. minimization and
> > equilibration? See
> > http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
> >
> > Mark
> > _______________________________________________
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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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