From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Aug 25 2015 - 03:01:36 CDT
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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