Re: [AMBER-Developers] pmemd external force

From: Sergio Decherchi at IIT <>
Date: Mon, 2 Oct 2017 11:40:01 +0200

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?

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 <
>> 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
>> _______________________________________________
>> AMBER-Developers mailing list
> _______________________________________________
> AMBER-Developers mailing list

AMBER-Developers mailing list
Received on Mon Oct 02 2017 - 03:00:02 PDT
Custom Search