Dear Justin, Thank you for your reply. I have some other questions,
1) Is it allowed to set nrexcl=0 in topology file in order to make every coarse-grained particles interact with each. 2) If it is allowed, then in [pairs] section, do I need to list all the pairs? For example, a linear chain with 10 beads: [ pairs ] 1 2 1 3 1 4 1 5 ...... 2 3 2 4 ...... 9 10 or it can recognize the 1-5 1-6 or above automatically. Thanks a lot Kind regards, Li ________________________________________ From: [email protected] [[email protected]] on behalf of Justin Lemkul [[email protected]] Sent: Tuesday, February 26, 2013 6:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] mdrun WARING and crash On 2/26/13 11:57 AM, [email protected] wrote: > Dear all, > > I got WARNING after mdrun, which says: > > "WARNING: Listed nonbonded interaction between particles 794 and 797 > at distance 3f which is larger than the table limit 3f nm. > > This is likely either a 1,4 interaction, or a listed interaction inside > a smaller molecule you are decoupling during a free energy calculation. > Since interactions at distances beyond the table cannot be computed, > they are skipped until they are inside the table limit again. You will > only see this message once, even if it occurs for several interactions. > > IMPORTANT: This should not happen in a stable simulation, so there is > probably something wrong with your system. Only change the table-extension > distance in the mdp file if you are really sure that is the reason." > > I don't quite understand the 'table limit 3f', what does it mean? That's a simple output typo, though it's somewhat important. The format is for a floating-point number, printed with 3 decimal places (%.3f). For some reason that's not coming through correctly, though it did in previous versions. > In our system, the bonded interactions is FENE, and the non-bonded LJ > interactions are between every coarse-grained beads by setting nrexcl=0 in > topology file. > There's some physical instability in the model that is causing the system to blow up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
