[gmx-users] Excessive compute time using PME

Jordi Camps jcamps at lsi.upc.edu
Thu May 19 13:13:41 CEST 2005


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.


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'.



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  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 59 87608 - Fax: +31 20 59 87610           |
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|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |

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