> Attilio Vargiu wrote: >> Hi All, >> I'm simulating a drug-DNA complex in water, with the AMBER force field >> and >> running GROMACS in parallel on 8 processors. >> After ~100 ps, I get the error here below: >> >> --------- >> Program mdrun, VERSION 3.3.1 >> Source code file: nsgrid.c, line: 226 >> >> Range checking error: >> Explanation: During neighborsearching, we assign each particle to a grid >> based on its coordinates. If your system contains collisions or >> parameter >> errors that give particles very high velocities you might end up with >> some >> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot >> put these on a grid, so this is usually where we detect those errors. >> Make sure your system is properly energy-minimized and that the >> potential >> energy seems reasonable before trying again. >> >> Variable ci has value 3035. It should have been within [ 0 .. 2940 ] >> Please report this to the mailing list ([email protected]) >> --------- >> >> It is not the first time I got this error, but I'm pretty sure the >> system >> is well equilibrated (I taken the starting structure from a previous 3ns >> long simulation, I do not see anything strange visualizing the traj, and >> the solute RMSD with respect to the initial configuration stays below >> 1.5 >> angs), and the potential energy is reasonable and with no drift. >> Sometimes I tried simply to restart the simulation from the previous >> "stable" point with coordinates, velocities and energy information >> (through tpbconv), and this had fixed the problem. >> Is not this a little bit strange? Could be a problem of the compiler? >> I'm using the fortran compiler intel9.0, the gnu c compiler, mkl-7.2 and >> mpich. > > Yeah that does sound weird. My first suspect would be MPICH - try LAM.
In fact, following the suggestion by Yang Ye I tried to use a time step of 1.5 fs instead of 2, but unfortunately the run stopped just some ps later... :-(. Now I am trying using 1fs, but the same simulation with 4 instead of 8 processors seems didn't crash after 200 ps. Furthermore, simply restarting the simulation with 8 procs from the last point overcame the problem. I think I'll try to install the LAM... many thanks, bye Attilio > > 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 > -- Attilio Vittorio Vargiu PhD Student in Statistical and Biological Physics SISSA/ISAS, via Beirut 2-4, 34100 Trieste, Italy Tel. 00390403787335 Fax. 00390403787528 ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ _______________________________________________ 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
