[gmx-users] Excessive compute time using PME

[David van der Spoel]

On Thu, 2005-05-19 at 13:13 +0200, Jordi Camps wrote:
> Hello,
> 
> 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
> 3.17128.
> 
> Thank you for yout help.
start with EM, if necessary with slightly larger box.
> 
> Sincerely,
> 
> -- 
> Jordi Camps Puchades
> Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> UPC-CIRI
> 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.
________________________________________________________________________
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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