Hello everyone,today I tried to simulate several small molecules, however I failed. The process is like this:
I got DRG.gro and DRG.itp files from the PRODRG website, and used the command "genbox" to obtain a random listed conf.gro of 33 phenol molecules. Then I include "ffgmx" and " DRG.ITP” to generate my topology file. The mdp file was got from the website and I changed some of its parameters. The .tpr file can be generated sucessfully, however, when I run command -mdrun, simulation crashed. tep 8 Warning: pressure scaling more than 1%, mu: -1128.98 -1128.98 -1128.98 Step 8, time 0.016 (ps) LINCS WARNING relative constraint deviation after LINCS: max 523474176.000000 (between atoms 102 and 103) rms 56971412.000000 bonds that rotated more than 30 degrees: Then I do em first before simulation. It still didn't work.Wrong information was like this: 5000 steps, 10.0 ps. Back Off! I just backed up run.trr to ./#run.trr.1# Back Off! I just backed up run.xtc to ./#run.xtc.1# step 90, remaining runtime: 161 s Section mistake Any help will be much appreciated. _______________________________________________ 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
