Hi Marc,<br>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 ?<br><br>With Thanks,<br>Vivek<br><br><div class="gmail_quote">
2008/11/6 Marc F. Lensink <span dir="ltr"><<a href="mailto:lensink@bigre.ulb.ac.be">lensink@bigre.ulb.ac.be</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d">On Thu, Nov 06, 2008 at 03:08:53PM +0530, Bhawana Gupta wrote:<br>
> hi,<br>
><br>
> i want to ask that how we can know that how much ns(1 ns or 2 ns.....20 ns),<br>
> we can run on our system which doing md simulations.<br>
> Means how we cme to know that if we go for 5 ns, then our system will not<br>
> hang or crash out.<br>
<br>
</div>very nice question...<br>
<br>
a crash you notice because the process died and/or there is no output<br>
written. use the -v option of mdrun and pipe it to a file. when the<br>
file is still being written, your job still runs.<br>
<br>
now for how long to simulate, you will have to find the perfect<br>
balance between 1) too short simulations have no biological relevance<br>
and 2) too long simulations deviate too much from reality because of<br>
imperfect parameters. so 3) always compare/compliment with experiment<br>
(if possible).<br>
<br>
cheers,<br>
marc<br>
<br>
<br>
--<br>
Marc F. Lensink<br>
Centre for Structural Biology and Bioinformatics CSBB<br>
Université Libre de Bruxelles <a href="mailto:marc.lensink@ulb.ac.be">marc.lensink@ulb.ac.be</a><br>
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium<br>
tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425<br>
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</blockquote></div><br>