[gmx-users] stable trajectory?

David van der Spoel spoel at xray.bmc.uu.se
Thu Aug 18 14:28:58 CEST 2005

On Thu, 2005-08-18 at 14:05 +0200, Ulrich Omasits wrote:
> Hi,
> I'm simulating a protein-ligand system in a 20A-SPC waterbox using the 
> gmx-ff and PME.
> My problem:
> The ligand should be high-affinity but in two out of five 
> one-nanosecond-simulations the ligand detaches the protein!
> In one simulation the ligand seems to be stable (RMSD & RMSF look nice) 
> but then the same simulation performed again (only starting velocities 
> differ) delivers totally different results (ligand even detaches!).
> How can this happen!?! What can I do?
> Should I change the forcefield, the water-type, the box-type, the 
> PME-parameters,...?
> Could these changes affect the trajectory such drastically?
How about your starting structure?

> Thanks
> Ulrich
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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://xray.bmc.uu.se/~spoel

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