[gmx-users] query about protein-ligand complex

[sangeeta]

I could not mail you as our net was down, 
you asked me "Is your system
 properly minimized? "
My question is how can I understand whether my system is properly minimised?
  the run is still going on, I can realize that something is going wrong. 
But I can not detect it.The log file is giving the error that the system is 
not properly minimised.I am giving you the messege,
"2127   2131  176.6  223178260480.0000 3921810030592.0000      0.1330
   2128   2129  176.6  69075034112.0000 1233987043328.0000      0.1000
   2128   2130  176.6  69075394560.0000 1233986912256.0000      0.1000
   2131   2132  176.5  69056528384.0000 1233902108672.0000      0.1000
   2131   2133  176.5  69054996480.0000 1233896734720.0000      0.1000
Constraint error in algorithm Lincs at step 9
 
t = 0.018 ps: Water molecule starting at atom 13339 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
Large VCM(group rest): -168597.92188, 112023.07031, -175543.56250, ekin-cm:  
3.95206e+15
"
 will you please give  me some suggestion , so that 
I can run the system from the beginning?
regards
Sangeeta


On Fri, 30 Jun 2006 14:50:44 +0200, Erik Marklund wrote
> 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 
> > Open WebMail Project (http://openwebmail.org)
> > 
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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
> 
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