root wrote:
Hello everyone,today I tried to simulate
several small molecules, however I failed. The process is like this:
Thank you for describing your process. This makes it much easier to help
you.
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.
In the vast majority of cases, this is essential. Search the mailing
list for other examples of successful and unsuccessful protocols.
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
Hmmm I've never seen that error before.
Mark
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