Hi Shay, sorry for the late comment - let me guess, you compiled Gromacs in double precision? :) Greetings Steffen
> < 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 >> > > > -- Dipl.-Chem. Steffen Wolf Fellow of the Ruhr-University Research School Department of Biophysics University of Bochum ND 04/67 44780 Bochum Germany Tel: +49 (0)234 32 28363 Fax: +49 (0)234 32 14626 E-Mail: [email protected] Web: http://www.bph.rub.de _______________________________________________ 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
