[gmx-users] query about protein-ligand complex

[Erik Marklund]

On Fri, 2006-06-30 at 17:52 +0530, sangeeta wrote:
> 
> Dear all,
> 
> I am trying to run the dynamics of protein-ligand complex following the 
> tutorial "GROMACS Tutorial for Drug_Enzyme Complex version 3.3.1"
> . I am running position restricted dynamics of the 91az8.pdb protein as 
> mentioned in the tutorial trp.pdb & drg.pdb)in a Linux server machine, I can 
> not understand why it is taking such a long time, the machine is not busy 
> with any other jobs.I ran it before & I stopped  the run at 1200 min, now it 
> is going for about 215 min, &  step6.pdb, step7.pdb etc files are being 
> formed, I can not undersyand whether I am doing any wrong step, why it is 
> taking such a long time , I don't know , please help.

stepX.pdb files are generated when things go wrong, for example when
forces or other quantities becomes NaN or Inf. The log files should give
some clues about what is happening to your system. Is your system
properly minimized? Please provide some more information, otherwise it's
difficult to help you.

/Erik Marklund

> 
> regards
> sangeeta 
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4537          fax: 46 18 511 755
erikm at xray.bmc.uu.se