From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Sep 22 2011 - 04:32:45 CDT
Hi Hasan,
There are two options:
1) write a TclForces script that calls loadTotalForces and writes them
to a file;
2) use the "collective variable" module and define Cartesian
coordinates as colvars (the distanceZ coordinate works for that) and
activate the outputSystemForce option.
In both cases, you may run into trouble if there are many atoms
involved and the files are output frequently: that could result in
excessively large files, and poor performance due to disk I/O. This
can be improved by making the Tclforces script write a binary file.
Alternately, depending on what you want to do with the forces, it
could be more efficient to do the analysis on-the-fly and write only
the results.
Jerome
On 22 September 2011 09:50, Hasan haska <hasanhaska_at_yahoo.com> wrote:
> Dear Namd users,
> I need to get net forces on each atom as a PDB output file for my
> simulations. Is it possible to get a force pdb file from NAMD simulations ?
> Please suggest and help. All help is truly appreciated.
>
> Thanks for your help.
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