On Fri, Jun 14, 2013 at 8:22 AM, ET <sketchfoot.gmail.com> wrote:
> Is there any way to output the forces a small molecule experiences within
> the simulation with minor adjustment of source code? Is this hopefully
> going to be a feature in a later version of AMBER? :)
>
If you want a trajectory of forces, my best suggestion would be to see
where the velocities are written to the mdvel file and dump the forces
instead of the velocities to that file (unless you need the coordinates,
forces, AND velocities -- then you'll need to duplicate what was done for
the crds and frcs to a separate file).
There are 'gotchas' in parallel, though, since the forces are not
distributed for every atom to the master necessarily... In pmemd you'll
need to call mpi_gathervec(atm_cnt, frc) in order to collect the forces to
the master node before writing. In sander I think if you modify
"parallel.h", the logtwo table to make every entry 0, then it will force
the fdist routine to use a 'reduce_scatter' call to communicate the forces,
which will result in a complete set of coordinates on the master thread
(the binary tree may do that as well, but I can't be certain).
If you want to do this in the CUDA code, you'll need to add a
gpu_download_frc call in order to synchronize the forces with the CPU to
print them out.
Note if you go the mdvel route, you will need to print to a NetCDF file and
then use some kind of NetCDF reader to extract the data (e.g., the netCDF4
Python module, your own custom C program that links to the netCDF API, or
parsing the output of ncdump).
HTH,
Jason
FWIW, I recall conversations with other developers that have indicated
their plans to include this as a feature in a future version of Amber due
to its increasing popularity.
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 14 2013 - 07:00:02 PDT
