Hi all,<br><br>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.
<br><br>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). <br><br>Who knows how to solve it? Thanks a lot.
<br><br><br>Program mdrun, VERSION 3.3.1<br>Source code file: nsgrid.c, line: 226<br><br>Range checking error:<br>Explanation: During neighborsearching, we assign each particle to a grid<br>based on its coordinates. If your system contains collisions or parameter
<br>errors that give particles very high velocities you might end up with some<br>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<br>put these on a grid, so this is usually where we detect those errors.
<br>Make sure your system is properly energy-minimized and that the potential<br>energy seems reasonable before trying again.<br><br>Variable ci has value -2147483648. It should have been within [ 0 .. 1000 ]<br>Please report this to the mailing list (
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>)<br>-------------------------------------------------------<br><br clear="all"><br>-- <br>****<br>Baofu Qiao<br><br>