[gmx-users] small molecules simulation

root sansanqin00 at mails.tsinghua.edu.cn
Tue Apr 10 18:29:44 CEST 2007

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

tep 8 Warning: pressure scaling more than 1%, mu: -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.

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