HI When I run MD, my system is exploding. And, I found after minimisation, the atoms of my molecule are seperated apart.
The overall charge of my system is +1, and I put one molecule in the gas phase to do the structure test. But, it was already exploding. Is it hard for a +1 charge molecule to maintain a good shape under MD simulation? What are the procedures to test and determine the mistakes I made? Thank you Lin Back Off! I just backed up md.log to ./#md.log.1# Getting Loaded... Reading file fullmd.tpr, VERSION 3.3.3 (single precision) Loaded with Money starting mdrun 'azoct' 100000 steps, 100.0 ps. Warning: 1-4 interaction between 11 and 18 at distance 1.301 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file step 10, will finish at Sun Oct 5 06:17:20 2008 ------------------------------------------------------- Program mdrun, VERSION 3.3.3 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. Variable ci has value -2147483648. It should have been within [ 0 .. 5832 ] ------------------------------------------------------- "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart) _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
