Re: call "NAMD" from another program

Date: Sat Jul 11 2015 - 22:21:09 CDT

It depends on the complexity of the jobs.
There may be a simple solution for some cases.

1. parallel jobs,
i.e. each job is independent with the other, and you just want run them one-by-one automaticly.
You can put the files of each job in separate folder, and run a SHELL command:
for i in ${PWD}/*/; do
    cd "$i"
    namd2 ... *conf > log
The SHELL command is much lighter than Python and much power than bat.

2. serial jobs,
e.g. annealing from 300K to 200K by 20K, each run for 10000 steps
You can use the workflow features by Tcl provide in conf file:
```tcl in conf file
for {set temp 300} {$temp <=200} {incr temp -20} {
    langevinTemp $temp
    run 10000

3. the input files are depends on the previous output files, but cannot use them directly.
Since each file is ascii, or could be translated to ascii, I think the `sed` and `awk` SHELL command could help you go through the full works.
From: Ma'Mon Hatmal
Date: 2015-07-10 06:53
To: namd-l
Subject: namd-l: call "NAMD" from another program
Hi All
I need to call "NAMD" (Molecular Dynamics program) by another program (like bat or python script) since it has an input file (config file) and output log file?, I need to call it for example 10 times (each time with a different input file)...would you please tell me if you have any idea.

How can we please call "NAMD" from another program? - ResearchGate. Available from: [accessed Jul 9, 2015].

Dr. Ma'mon Hatmal
PhD and MSc in Biochemistry and Molecular Biology
MSc in Global Medicine
BSc in Medical Laboratory Sciences

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