Replica exchange MD with NAMD with SGE....

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Fri Feb 25 2011 - 15:14:19 CST

• Next message: Ranyere Deyler: "Paratool`s error reading single point calculation."
• Previous message: Ye Yang: "Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation"
• Next in thread: Guoxiong Su: "Re: Replica exchange MD with NAMD with SGE...."
• Reply: Guoxiong Su: "Re: Replica exchange MD with NAMD with SGE...."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.

• Next message: Ranyere Deyler: "Paratool`s error reading single point calculation."
• Previous message: Ye Yang: "Hi, I am a new user of Namd, and I met some problems using increment of temperature during simulation"
• Next in thread: Guoxiong Su: "Re: Replica exchange MD with NAMD with SGE...."
• Reply: Guoxiong Su: "Re: Replica exchange MD with NAMD with SGE...."
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:56:41 CST