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. Thanks in advance, ciao Attilio -- 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
