< Is this reproducible? Yes. I've taken the same simulation and had it re-run and got the same error at the exact same frame (frame 693, which is timeframe 6930).
<You could try to fork off a tpr file using tpbconv -f -e -s -o just <before this happens and rerun it. I did something similar to what you suggest before posting here: Oddly enough the Warning did not occur: I ran the simulation up to 6000ps and then continued the simulation to another 4000ps and the simulation ran correctly and without any problems. < It can also be combined by input parameters, e.g. too large time step, <too infrequent neighborsearching etc., use of cutoffs. If no other suggestions I'll try working that angle too, since a lot of my simulations are running with very similar mdp parameters without problems. Thanks again for your prompt reply, -Shay Shay Amram wrote: > Of course. I'm using version 3.3.3 of GROMACS. > -Shay > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Mark Abraham > Sent: Tuesday, December 30, 2008 02:59 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Forces are large - How to track down the culprit > > Shay Amram wrote: >> Greetings dear Gromacs users, >> >> >> >> I have recently been simulating a POPG membrane* in water (SPC). Several >> of my simulations after running well into the 10ns and 20ns are >> sometimes getting a "Forces for atom X are large". >> >> I'm rather unsure as to the cause of this situation. Moreover, as far as >> I can tell from viewing the simulation, the system _does NOT_ explode >> (as may be suggested by wiki.gromacs and some previous answers to this >> kind of situation). The rest of the simulation looks much as it did in >> the beginning. >> >> I would be interested (and thankful!) to hear any of your opinions as to >> why I'm getting this message (or how to catch the culprit), and more >> importantly, how to prevent it from happening in the future. > > During this version-transitive period, it's always right to report the > GROMACS version that you're using. It would normally be right to be > using the most recent version (4.0.2) if encountering problems. > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > _______________________________________________ > gmx-users mailing list [email protected] > 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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [email protected] [email protected] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] 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
