From: Vermaas, Joshua (
Date: Sun Feb 18 2018 - 12:09:02 CST

But it isn’t called. Source it within the file. Within “main_job.conf”, you need to have a “source normal_job.namd” command, otherwise NAMD won’t read in and evaluate the contents of normal_job.namd.

Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory<>

On Feb 16, 2018, at 5:42 AM, Srijita Paul <<>> wrote:

Thanks Souvik, the problem is solved according to your suggestion. But now I am geting another error -
ERROR: 'cutoff' is a required configuration option
ERROR: cutoff defines: local electrostatic and Vdw distance
ERROR: 'exclude' is a required configuration option
ERROR: exclude defines: Electrostatic and VDW exclusion policy
ERROR: 'outputname' is a required configuration option
ERROR: outputname defines: prefix for the final PDB position and velocity filenames

while the normal_job.namd file already contains those informations and that file already exists in the working directory.

On Tue, Feb 13, 2018 at 6:02 PM, Souvik Sinha <<>> wrote:

For tcl inline comment, you have to use " ; " separator before the start of the comment. So in your main_job.conf, this correction may help:

set num_runs 50000000 ; # (100ns job)


On Tue, Feb 13, 2018 at 4:36 PM, Srijita Paul <<>> wrote:

I am trying to start REMD in NAMD. After executing the job I am getting such type of error
/cm/local/apps/slurm/var/spool/job189102/slurm_script: line 15: file##: command not found
------- Partition 8 Processor 0 Exiting: Called CmiAbort ------
Reason: REPLICA 8 FATAL ERROR: wrong # args: should be "set varName ?newValue?"
    while executing
"set num_runs 10000 # (20ns job)"
    (file "main_job.conf" line 6)
My configuration files are attached here. Is there any problem in configuration file or it is a problem in MPI script file?

                              Thank you

Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275

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