[gmx-users] Energy Minimization Problem

[David van der Spoel]

Robson P. S. Peguin wrote:
> Hi everybody,
> 
> I'm trying to simulate an interfacial system using Gromacs. My simulation box has water in one side and hydrofluorocarbon in the other side. This system was successfully tested using DL-POLY simulation package  previously. Also, the box containing pure hydrofluorocarbon worked fine using Gromacs. However, when I try an energy minimization simulation with the interfacial system, after a couple of steps (~400), the geometry of the hydrofluorocarbon changes. I mean, the molecules begin to lose bonds or atoms. It didn't collapse the box yet, but I can see from a visualization package that the molecules are distorted. I tried to decrease the timestep unsuccessfully. If you have any suggestions, I'll be happy to know them.
> 
probably an issue in the topology.
send the relevant bits to the list please.
> thanks
> 
> Robson
> 
> --
> Robson Peguin, PhD Student
> Wayne State University, ChE
> Detroit - MI, 48201 - USA
> 2015 MEB, (313) 577-1416
> 2348 ENG, (313) 577-5765
> Fax: (313) 577-3810
> e-mail: robson_peguin at wayne.edu
> http://chem1.eng.wayne.edu/~sdr/
> _________________________________________________
> Robson P. S. Peguin, PhD Student
> Wayne State University
> Department of Chemical Engineering and Materials Science
> Detroit - MI, 48201 - USA
> 2015 MBE, phone: (313) 577-1416
> 2348 ENG, phone: (313) 577-5765
> Fax: (313)577-3810
> e-mail: robson_peguin at wayne.edu
> http://chem1.eng.wayne.edu/~sdr/
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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