[gmx-users] how much ns

[Marc F. Lensink]

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