[gmx-users] sridhar-problem with Position Restrained Dynamics run.
christoph.freudenberger at chemie.uni-ulm.de
Sun Apr 27 10:14:00 CEST 2003
Most likely you have a problem with pressure scaling.
tau_p is to tight and the system starts to oszillate.
Use values of 5-20 for an unequilibrated system.
You can reduce the value when the box is scaled and
stable but even then tau_p<1 usally will not work.
> 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.
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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