Gaurav Chopra wrote: > Hi > > I am doing a steepest descent for the initial mdrun for a peptide and it > gives me the following error. Please advice. > > Thanks > Gaurav > ------------------------------------------------------- > Program mdrun, VERSION 3.3 > 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. Please follow the advice in the above two sentences. Check your structure. I did the energy minimization by increasing the number of steps using steepest descent, nothing happened. Then I tried cg using -DFLEXIBLE and steep using -DFLEXIBLE in my mdp file and I was able to compute using mdrun but I got the following in my log file Initiating Steepest Descents Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest, initial mass: 24594 Started Steepest Descents on node 0 Mon Mar 13 17:07:04 2006 Removing pbc first time Done rmpbc Steepest Descents: Tolerance (Fmax) = 1.00000e+01 Number of steps = 10000 Grid: 10 x 10 x 20 cells Configuring nonbonded kernels... Testing AMD 3DNow support... not present. Testing ia32 SSE support... present. Then with this when I do position restrained md, using -DPOSRES in mdp file for grompp and md integrator and then mdrun for position restrained I get the following Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1391229833052160.000000 (between atoms 655 and 657) rms 40665803128832.000000 bonds that rotated more than 30 degrees: also segmentation fault. Is there a different method to do energy minimization better as suggested in the range check error warning. Thanks Gaurav > > Variable ci has value -2147483648. It should have been within [ 0 .. 2000 ] > Please report this to the mailing list (gmx-users at gromacs.org) > ------------------------------------------------------- > > _______________________________________________ > gmx-users mailing list gmx-users at gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-request at gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
