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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Received on Mon Oct 02 2017 - 02:00:02 PDT
