Thanks very much Jason! :) Will have a chat with my colleague who deals
more with the coding. This will be very useful.
br,
g
On 14 June 2013 14:30, Jason Swails <jason.swails.gmail.com> wrote:
> 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 - 07:30:02 PDT
