The forces I get there can come from a GPU explicit solvent computation
or are just from a CPU run?
>>So far just CPU. I haven't been brave enough to mess around with the GPU
code, even to the extent of just forcing a download/upload of forces and
coordinates.
>>Please let me know how you get on, when I started emil, pmemd.CUDA was
still hot off the press.
What about the units?
>>The forces in pmemd seem to be in "AMBER units"
http://ambermd.org/Questions/units.html . (kcal/mol/A).
Josh
On 2 October 2017 at 11:40, Sergio Decherchi at IIT <sergio.decherchi.iit.it
> wrote:
>
> Thanks Josh,
> "call emil_step(..." should be the right entry point.
> The forces I get there can come from a GPU explicit solvent computation
> or are just from a CPU run?
> What about the units?
> Best,
> sd
>
> Il 02/10/2017 10:53, Josh Berryman ha scritto:
> > I have already found hooks to add an extra force to pmemd, for the
> purpose
> > of the emil module in which thermodynamic integration is performed wrt a
> > simplified reference hamiltonian for the molecule.
> >
> > Have a look at the hooks in runmd.f90 etc where I take forces in and out
> of
> > pmemd.
> >
> > Josh
> >
> > On 2 October 2017 at 10:35, Sergio Decherchi at IIT <
> sergio.decherchi.iit.it
> >> wrote:
> >> Dear Amber Developers,
> >> I would like to add an external force to the pmemd program.
> >> I am looking at the pme_force.F90 source file and it seems a suitable
> >> location where
> >> to add an external force because I see that there, for instance, scaled
> >> md is applied.
> >> Is this correct?
> >> Also I am calling gpu_download_crd and gpu_download_frc to download
> >> coordinates and forces
> >> and I update them upon computation via gpu_upload_frc. Is this the right
> >> approach? Which
> >> are the units of the forces and coordinates used by thoose functions and
> >> which is the memory layout of those arrays?
> >> Is there a more lightweight way to retrieve forces/coordinates from GPU,
> >> because I observed a significant slow down
> >> when using those functions at each time step.
> >> Last, in case one may envision to add the force directly on the GPU (to
> >> make it faster) which is the memory layout of the forces on the GPU and
> >> which are the variables that should be updated/read (e.g. coordinates,
> >> forces)?
> >> Many thanks,
> >> Sergio Decherchi
> >>
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> >>
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Received on Mon Oct 02 2017 - 03:30:01 PDT
