On Tue, Dec 11, 2007 at 12:44:28PM +0100, Magnus Andersson wrote: > Hi all, > > My constrained 20ps simulation crashes for some reason. This simulation is > very much alike other simulations I've run in a successful manner > previously. Seems like there is a probem on atoms constituting an > artificial membrane... > > Anyway, I guess it is a general question. Where do you start looking if > the run crashes like this (and a slightly different system, just strctural > change, it has exactly the same atoms...)?
sometimes the system is caught in a deep and steep energy well with wide barriers so that the assignment of new velocities also doesn't work. if the system is constructed from a previous simulation, find a few time frames before and re-construct. otherwise i suppose you could identify the faulty atom and delete the nearest water molecule. cheers, marc -- Marc F. Lensink Centre for Structural Biology and Bioinformatics SCMBB 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
