[gmx-users] how much ns
viveksharma.iitb at gmail.com
Fri Nov 7 06:23:48 CET 2008
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 ?
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
> > 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
> > 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).
> 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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