[gmx-users] Windows Gromacs Issue

[Raj Badhan]

Dear David,
If I had a bad starting structure, would the position restrained and 
energy minimisations that I carried out not pick this up?

Subject:        	Re: [gmx-users] Windows Gromacs Issue
From:           	David <spoel at xray.bmc.uu.se>
To:             	gmx-users at gromacs.org
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Date sent:      	23 Nov 2003 09:59:41 +0100

> On Sat, 2003-11-22 at 21:09, Raj Badhan wrote:
> > Dear All,
> > I'm running a simulation of a protein in the windows version of 
> > gromacs.
> > I have three versions of the same protein, and am running version 1 
> > on one PC (500ps simulation) which is running fine.
> > I run version number two, and when initiating the final MDRUN to 
> > start the simulation, mdrun gets to the point of :
> > 
> > starting mdrun:
> > 250000 steps etc....
> > 
> > Before backing up the trr files and exiting with:
> > 
> > Back off! Just backup step0.pdb to ......
> > Wrote PDB with previous and current coordinates
> 
> bad starting structure
> 
> > 
> > before the the command prompt crashes saying MDRUN caused it 
> > to end.
> > I have run this simulation on two PC (windows XP) and they both 
> > end the same way, and I have no idea why.
> > (The 20ps position restrained sim. works OK too).
> > Any ideas?
> > Many thanks
> > Mr Raj Badhan
> > School of Pharmacy and Pharmacetical Science
> > The University of Manchester
> > Manchester, UK.
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> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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Mr Raj Badhan
School of Pharmacy and Pharmacetical Science
The University of Manchester
Manchester, UK.