Re: Net forces on each atom can be written to PDB in NAMD 2.8b1

From: Jim Phillips (
Date: Mon Mar 28 2011 - 12:00:59 CDT

You can do something like this to get a PDB file myfile.force at step 0:

binaryoutput off # must be before any run/minimize commands
run 0
output onlyforces myfile

The run 0 is needed so that there are calculated forces to output. You
can change it to whatever you want. You can also run some other number of
steps or have multiple run commands if you like.


On Mon, 28 Mar 2011, oguz gurbulak wrote:


Dear All,
> I’ve just learned that  it’s possible to get a force output file in NAMD
2.8b1.  I installed NAMD 2.8b1 and wanted
to get the force output file. I got the net forces on each atom as a DCD
trajectory file. And now I also want to do it using the Tcl output command “output
withforces basename” and get a final PDB file. But I haven’t got enough
information about using Tcl output commands. Could you please help me to learn
this procedure ? How can I do it ?

Thank you very much for your attention.

Kind regards.

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