From: Ehsan Ban (ehsan.ban_at_gmail.com)
Date: Thu Sep 22 2011 - 05:18:34 CDT
By setting the two parameters forceDCDfile & forceDCDfreq a dcd file for
the forces of all the atoms can also be outputted.
On Thu, Sep 22, 2011 at 5:32 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> 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.
> 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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