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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Prof. Raphaël TERREUX
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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/>
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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
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P-HPMob
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Received on Tue Apr 05 2016 - 02:30:02 PDT
