[gmx-users] small molecules simulation

Mark Abraham Mark.Abraham at anu.edu.au
Tue Apr 10 19:17:13 CEST 2007

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 

> 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.

> 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.


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