Sorry... the exact number is the one in inpcrd files.... I have no problem with pmemd....
My problem is how to minimize the system prior uses pmemd.
-----Message d'origine-----
De : Gould, Ian R [mailto:i.gould.imperial.ac.uk]
Envoyé : mardi 5 avril 2016 11:13
À : AMBER Mailing List
Objet : Re: [AMBER] sander number of atoms limit
Dear Raphael,
We routinely run systems which are greater than 1M atoms, currently our largest is 1.8M atoms, we run these on the cuda version of pmemd. You say in your e-mail that the size is exactly 1,149,859 however you inpcrd says 1,158,949 which is bigger and I think this is your problem with sander. Check that your number of atoms in the parm file you are using matches the number of atoms in the inpcrd.
Cheers,
Ian
--
Dr Ian R Gould, FRSC.
Reader in Computational Chemical Biology Department of Chemistry Imperial College London Exhibition Road London
SW7 2AY
E-mail i.gould.imperial.ac.uk
http://www3.imperial.ac.uk/people/i.gould
Tel +44 (0)207 594 5809
On 05/04/2016, 09:59, "TERREUX RAPHAEL" <raphael.terreux.univ-lyon1.fr> wrote:
>Hi,
>
>I am trying to make a MD of a large system which exceed 1 M atoms (1,149,859 exactly). I used sander just for minimizing the system before used pmemd.
>If pmemd and pmemd.cuda has a limit to few millions atoms, sander or its file format used seems to have 999.999 atoms limits.
>When the minimization ended the first two lines of the crd files are changed from :
>
>default_name
>1158949
>80.3846739 199.1308729 115.0638892 79.5031396 199.3859663 114.6420770
>...
>
>To
>
>defa
>******
> 80.8650585 199.3545504 114.9412061 79.8759488 199.6309180 114.8514299
>...
>
>Imin=1 seems not work on pmemd (which is logical)
>How could minimize a system with more than 1M atoms on amber 14/ambertools 15
>Thanks in advances
>
>Raphael Terreux
>
>
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Received on Tue Apr 05 2016 - 02:30:05 PDT
