Hi all, Now I meet a problem when building a system. I used prodrg to get the .pdb of a single molecule, write the .top file manually. The single-molecule system is equilibriumed (em, NVE, NTV,NTP are all ok for at least 1 ns). Then I used two method to get a bigger (8 molecules) system: 1) genbox -cs -box; 2) genbox -nmol -ci -cp. Both result are ok when EM. But when NVE is runn, result 2 crashed right now . For results 1, NVE is ok, and short-time NTV and NTP(about 10ps) are ok, but long-time NTV and NTP(1ns) crashed with the same reason.
On the other hand, I build a very dilute sytem (5 molecules, density is about 2 g/l). It runs very well. But the problem is it is very hard to converge to the suitable density (1000 g/l). Who knows how to solve it? Thanks a lot. 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 -2147483648. It should have been within [ 0 .. 1000 ] Please report this to the mailing list (gmx-users@gromacs.org) ------------------------------------------------------- -- **** Baofu Qiao
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