Ok so it’s not that. To the best of my knowledge there are no restrictions on the size of system that sander can handle, it looks like a formatting issue of the output, are both coordinate files the same size? That is the same number of lines? I assume that it’s a periodic box simulation? If so you have ntb=1?
On 05/04/2016, 10:16, "TERREUX RAPHAEL" <raphael.terreux.univ-lyon1.fr> wrote:
>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
>>
>>
>>*************************************************************
>>Prof. Raphaël TERREUX
>>---------------------------------------------------------
>>Tel +33 (0)4 37 65 29 43 Fax +33 (0)4 72 72 26 04
>>PRABI-LG / Laboratoire de Biologie Tissulaire et d'Ingénierie (LBTI) - UMR 5305 CNRS - Université Lyon 1.
>>Institut de Biologie et Chimie des Protéines (IBCP)
>>7, passage du Vercors - 69367 Lyon - FRANCE
>>http://www.ibcp.fr<http://www.ibcp.fr/>
>>----------------------------------------------------------
>>Tel: + 33(0)4 78 78 56 00 Fax: +33(0)4 78 78 56 06
>>Département pédagogique des Sciences Physico-Chimiques et Pharmacie Galénique.
>>Faculté de Pharmacie (ISPB) http://ispb.univ-lyon1.fr<http://ispb.univ-lyon1.fr/>
>>8 avenue Rockefeller, 69373 Lyon Cedex 08, FRANCE
>>************************************************************
>>P-HPMob
>>
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Received on Tue Apr 05 2016 - 02:30:07 PDT
