Questions on calling external program to calculate force with NAMD

From: Wasut Pornpatcharapong (
Date: Mon Feb 10 2014 - 15:41:48 CST


I am currently trying to set up an AIMD calculation with NAMD, and I would
like to call NWChem as a force calculating package. However, when I try to
read the documentation on this part, I am not sure about the syntax
structure for the configurations. Below are my questions,

1.) I am currently working on cascade supercomputer at PNNL, and they use
SLURM scheduler. I wonder if I can simply put 'srun ....' in
'extForcesCommand'? If I can't, how do I need to put a proper command to
call NWChem?

2.) In what way does the 'extCoordFilename' work? Does it need to exist
alongside 'extForceCommand'? I am not quite clear on this, and I plan to
use tcl script to generate an input for NWChem instead, but I wonder if I
could forgo 'extCoordFilename'?

3.) Upon calling NWChem, how are the resources distributed? Do all the
cores stop suddenly and take part in NWChem calculations instead until they
finish and then resume the dynamics in NAMD?

4.) Could you please explain more to me on the format of the file to be
used in 'extForceFilename'? What kind of energy do I need to put into the
first line? Does 'fx fy fz' actually mean the actual force on x, y, and z
directions of each atom that I have to replace? Do I really need the virial
coefficients in the file?

Thank you,

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