Problem of running NAMD

From: Yingzhe Liu (yingzhe.cn_at_gmail.com)
Date: Wed Dec 08 2010 - 04:37:45 CST

• Next message: Jun Zhang: "SHAKE convergence property for CUDA and nonCUDA NAMD"
• Previous message: JC Gumbart: "RE: Free energy perturbation (FEP) hybrid pdb file"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Dear NAMD users,

How to modify the script of spawn_namd.tcl to run the example
of REMD which is included in the NAMD software.

The version of NAMD used in our cluster is 2.7b2.
The platform of NAMD is Linux-x86_64-ibverbs (InfiniBand via
OpenFabrics OFED, no MPI needed). The following command line
is used to run conventional MD simulation.

charmrun namd2 +pN ++nodelist $nodelist $conf > $log

Any information will be appreciated!

Best regards,

yingzhe

-- 
Yingzhe Liu
   Ph.D. Student of Analytical Chemistry
 Chemistry Department, Nankai University
 Tianjin, P.R.China, 30071
 Tel: +86-022-23509425
Web: http://chinfo.nankai.edu.cn/

• Next message: Jun Zhang: "SHAKE convergence property for CUDA and nonCUDA NAMD"
• Previous message: JC Gumbart: "RE: Free energy perturbation (FEP) hybrid pdb file"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:50 CST