AW: Problem running REMD simulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 25 2015 - 03:50:15 CDT

 

 

I only have experience with the self-compiled mpi builds which were required in earlier versions of namd to enable replicas. If I understood the current development there are precompiled builds of namd now, that support +replica, too. I guess they have „multicopy“ in its name.

 

 

Norman Geist

 

Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Nicholus Bhattacharjee
Gesendet: Dienstag, 25. August 2015 10:02
An: namd-l_at_ks.uiuc.edu
Betreff: namd-l: Problem running REMD simulation

 

Hello,

I am reposting the query as I have not got any reply.

 

I am trying to run REMD simulation using NAMD. I am following the suggestions given in

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node66.html

I did the following

example$ mkdir output
example$ cd output
output$ mkdir 0 1 2 3 4 5 6 7
output$ cd ..
example$ mpirun /usr/local/NAMD_2.9_Linux-x86_64-multicore/namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log

I got the error message
%%%%%%%%%%%%%%%%%%%%%%%%%%%
FATAL ERROR: Unknown command-line option +replicas
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Unknown command-line option +replicas

Charm++ fatal error:
FATAL ERROR: Unknown command-line option +replicas
%%%%%%%%%%%%%%%%%%%%%%%%%%

The second part of the question is about running REMD using AMBER topology file.

For running normal simulation we change in the configuration file

"structure XXX.psf" by

amber yes

parmfile XXX.top"

Now in REMD configuration file what we change for the following line

set psf_file "XXX.psf"

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