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AMBER 12 AmberTools 13
Tags amber, md
Edited Feb 7, 2014 6:50 PM by Frank Beierlein
AMBER 12 AmberTools 13
< Software used at the CCC < AMBER overview -----------------------(This first section is still experimental - please tell me if anything doesn't work.)
To use interactive tools like xleap, ptraj, antechamber (AmberTools 13) etc. on machines like ccc138:
Type the following command (should be found automatically, as it is in /ccc/SOFT/bin) to get the path and AMBERHOME set correctly: u s e A m b e r 1 2 A T 1 3 . c s h
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AMBER 12 AmberTools 13
You can then run sander.MPI or pmemd.MPI interactively on e.g. 4 processors using / u s r / l i b 6 4 / m p i / g c c / o p e n m p i / b i n / m p i r u nn p4s a n d e r . M P I . . . or / u s r / l i b 6 4 / m p i / g c c / o p e n m p i / b i n / m p i r u nn p4p m e m d . M P I. . . As far as I know, nobody has bothered yet to compile Amber12 using IFORT.
To run sander/pmemd interactively and to use interactive tools like xleap, ptraj, antechamber (AmberTools 13) etc. on eamon[1-3] (if you are sitting in EAM):
You need to amend your .cshrc or your .login first: s e tp a t h=($ p a t h/ h o m e / b e i e r l / s o f t w a r e / a m b e r 1 2 / b i n) s e t e n vA M B E R H O M E/ h o m e / b e i e r l / s o f t w a r e / a m b e r 1 2
If you want to use Amber in parallel, e.g. on 4 CPU cores, you can also add (this is only needed to do the tests) s e t e n vD O _ P A R A L L E L' / u s r / b i n / m p i r u nn p8 '
You can then run sander.MPI or pmemd.MPI interactively on e.g. 4 processors using / u s r / b i n / m p i r u nn p4s a n d e r . M P I. . . or / u s r / b i n / m p i r u nn p4p m e m d . M P I. . .
http://ccca140/groups/ccc/wiki/80d19/AMBER_12_AmberTools_13.html
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