[gmx-users] Excessive compute time using PME
David van der Spoel
spoel at xray.bmc.uu.se
Thu May 19 14:31:12 CEST 2005
On Thu, 2005-05-19 at 13:13 +0200, Jordi Camps wrote:
> I have some news about the problem. Yesterday I saw that the input that I
> was feeding was not completely contained in the octahedron, so I recentered
> the travelling waters and now I have a true octahedron as input for mdrun.
> If I chech the coordinates of the tpr file (extracted with editconf) I
> continue seeing an octahedron in VMD.
> But when I run the simulation with mdrun, it fails. And before core dumping,
> mdrun writes two files: step-1.pdb and step0.pdb.
> Step0.pdb shows an exploded molecule (and waters).
> Step-1.pdb shows my input in cubic boundaries. I think that this is the
> problem. I'm feeding an octahedron and mdrun is interpreting this like a
> box. There are some special considerations I should take into account if I
> want to simulate with an octahedron? Perhaps I'm missing some parameter in
> the grompp.mdp file? The box vectors, like the ones that I have in the file,
> are 6.72730 6.34256 5.49282 0.00000 0.00000 2.24243 0.00000 -2.24243
> Thank you for yout help.
start with EM, if necessary with slightly larger box.
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> c/. Jordi Girona 1-3
> Modul C6-E201 Tel. : 934 011 650
> E-08034 Barcelona Fax : 934 017 014
> Catalunya (Spain) e-mail: jcamps at lsi.upc.edu
> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> nombre de Anton Feenstra
> Enviado el: jueves, 19 de mayo de 2005 7:45
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Excessive compute time using PME
> Jordi Camps wrote:
> > Hello list!
> > Yes, you were right on the problem. I computed bad box vectors which
> > makes the box extra-large. Now I reduced the box to it's real size,
> > but now I get some kind of error. GXM writes an step-1.pdb and a
> > step0.pdb files (the second one shows that all the molecules exploded)
> > and core dumps. I'm working to find the cause.
> Loook at your periodic boundaries. If you changed the box size, you may
> well have (bad) overlap at the 'edges'.
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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