[gmx-users] sridhar-problem with Position Restrained Dynamics run.

David spoel at xray.bmc.uu.se
Sun Apr 27 11:15:01 CEST 2003

On Sun, 2003-04-27 at 12:04, Mr.Sridhar wrote:
> Dear GMX users,
> I am running dynamics of a KINASE protein. It contains two zinc ions and a
> Phorbol residue for which i could generate topology using PRODRG server.
> I ran smoothly till minimization. I created .tpr file by grompp for
> position restrained dynamics. But when I ran mdrun the program crashed
> giving some message which I could not get.
Check energies after minimization. If you have high (positive) energy
terms you probably have an error in your topology, or you have to
minimize even more.
> I am attaching the logfile and input mdp files. I'll be grateful to you if
> anyone of you can send me suggessions.
> regards,
> sridhar
Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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