AMBER Archive (2008)

Subject: AMBER: PMEMD and sander.MPI

From: Germain Vallverdu (germain.vallverdu_at_lcp.u-psud.fr)
Date: Tue Sep 09 2008 - 08:50:40 CDT

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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