> 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 .. 3375 ] > > Please report this to the mailing list ([email protected]) > > -------------------------------------------------------
I have seen this error when I have somehow generated bad contacts in my starting structure, causing atoms to explode of into space. Did mdrun generate any step*.pdb files? Those might give you some indication as to where the problem lies. > ----------------------------------------------------------------------------------------------------------------------------------------- > t= 0.02ps Water molecule starting at atom 71500 can not be settled. > Check for bad contacts and/or reduce the timestep.Wrote pdb files with > previous and current coordinates > ------------------------------------------------------------------------------------------------------------------------------------------- > I have triend reducing the time step and I still get the same error. > I have also pasted the pr.mdp file I use to set up and run position > restrained dynamics. Have you tried looking at the water molecule that contains atom 71500 to see what it might be bumping into? Again I suspect bad contacts. -Justin ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
