[gmx-users] how much ns

[vivek sharma]

Hi Marc,
Can you give an approximate time estimate for too short and too long time of
simulation, if I am running simulation for protein in water to see the
conformational changes ?

With Thanks,
Vivek

2008/11/6 Marc F. Lensink <lensink at bigre.ulb.ac.be>

> On Thu, Nov 06, 2008 at 03:08:53PM +0530, Bhawana Gupta wrote:
> > hi,
> >
> > i want to ask that how we can know that how much ns(1 ns or 2 ns.....20
> ns),
> > we can run on our system which doing md simulations.
> > Means how we cme to know that if we go for  5 ns, then our system will
> not
> > hang or crash out.
>
> very nice question...
>
> a crash you notice because the process died and/or there is no output
> written.  use the -v option of mdrun and pipe it to a file.  when the
> file is still being written, your job still runs.
>
> now for how long to simulate, you will have to find the perfect
> balance between 1) too short simulations have no biological relevance
> and 2) too long simulations deviate too much from reality because of
> imperfect parameters.  so 3) always compare/compliment with experiment
> (if possible).
>
> cheers,
> marc
>
>
> --
> Marc F. Lensink
> Centre for Structural Biology and Bioinformatics          CSBB
> Université Libre de Bruxelles           marc.lensink at ulb.ac.be
> Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
> tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425
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