Re: Replica exchange MD with NAMD with SGE....

From: Guoxiong Su (
Date: Wed Jul 13 2011 - 17:50:57 CDT


I am wondering how you can get the replica exchange MD work serially on the
SGE system. I have already made REMD parallel on the PBS system and IBM
power clusters. Maybe I can help you with it.

Yours sincerely,
Guoxiong Su

On Fri, Feb 25, 2011 at 3:14 PM, Raul Araya <> wrote:

> Dear NAMD users:
> We are trying to use REMD with NAMD on our cluster that uses SGE for
> quequeing the jobs. Until know we have only been able to allow one replica
> per core. Wat we need however is to allow that each replica can be simulated
> with multiple cores. Can any one help us with these? It seems that the
> examples provided in the file "spawn_namd.tcl" are onluy useful when
> using charmmrun for parallel processing.
> Cheers.
> Raúl Araya Secchi
> B.Sc Molecular Biotechnology.
> Molecular Biotechnology Engineer.
> PhD Student (Biotechnology Program. UNAB, Chile)
> Computational Biology Lab (DLab)
> Center for Mathematical Modeling (CMM)
> Facultad de Ciencias Físicas y Matemáticas.
> Universidad de Chile.

Guoxiong Su
Cheung group
Department of Physics
University of Houston

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