It's a little bit challenging trouble I've got into! Of course for me. Thanks for your suggestions.
Sincerely, Shima ----- Original Message ----- From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Saturday, July 28, 2012 7:23 PM Subject: Re: [gmx-users] Re: system blowing up On 29/07/2012 12:51 AM, Dr. Vitaly V. G. Chaban wrote: >> Thanks for your reply. >> >> I'm following the protocol of Diagnosing an unstable system. Corresponding >> the first step I changed th nstxout to 1 for 3 times. >> The first and second time I got error the same as before ( some interactions >> seem to be assigned multiple times ) and it the warning as below was >> appeared: >> >> Warning: 1-4 interaction between 5 and 18 at distance 2.017 which is larger >> than the 1-4 table size 2.000 nm >> >> For the third time, I did'nt get any error and the output files were >> generated without any warning or error. >> >> >> Is it acceptable to go on with these outputs? Why such a thing happened? Is >> the system minimized sufficiently after 2 times? >> > > decrease your time-step That's not likely to help if there's an initial bond of length 0.35nm. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
