[gmx-users] Windows Gromacs Issue

[David]

On Sun, 2003-11-23 at 11:14, Raj Badhan wrote:
> Dear David,
> If I had a bad starting structure, would the position restrained and 
> energy minimisations that I carried out not pick this up?
not necessarily, but please check the energies in the log files from em
and PR (and MD). For a protein in water Epot should be < -42*Nwater,
and all the bonded should be rather small...

> 
> Subject:        	Re: [gmx-users] Windows Gromacs Issue
> From:           	David <spoel at xray.bmc.uu.se>
> To:             	gmx-users at gromacs.org
> Organization:   	Send reply to:  	gmx-users at gromacs.org
> 	<mailto:gmx-users-request at gromacs.org?subject=subscribe>
> 	<mailto:gmx-users-request at gromacs.org?subject=unsubscribe>
> 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.
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > -- 
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> 
> 
> Mr Raj Badhan
> School of Pharmacy and Pharmacetical Science
> The University of Manchester
> Manchester, UK.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++