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 <[EMAIL PROTECTED]> > 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 [EMAIL PROTECTED] > Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium > tel: +32 2 650 5411 secr: +32 2 650 2013 fax: +32 2 650 5425 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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