Hello AMBER !
I am trying to do NPT simulations with PMEMD. Then I ran two identical
simulations, one with sander.MPI and one with PMEMD to see differences
beetwen them.
Firstly, I do not understand why ewald parameters are not the same :
sander gives :
NFFT1 = 60 NFFT2 = 72 NFFT3 = 72
PMEMD gives :
NFFT1 = 56 NFFT2 = 70 NFFT3 = 72
The AMBER manual said that if one decrease NFFT1,2,3 this leads to
faster calculations but less accurate. Nevertheless, are this
differences relevant ? And why sander and PMEMD do not give the same
size of the grid ?
A more general question : is pmemd faster than sander.MPI thanks to
algorithm or is pmemd less accurate than sander ?
Thanks
Germain
--
Germain Vallverdu
Laboratoire de Chimie Physique
Université Paris Sud 11
germain.vallverdu.lcp.u-psud.fr
01 69 15 30 38 / 06 88 59 08 87
Chacun de nous a son étoile. Suivons la en nous félicitant de la
voir chaque jour un peu plus loin ! (V. Grignard)
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Received on Wed Sep 10 2008 - 06:07:43 PDT
