Re: [AMBER] problem of GPU with ibelly

From: David A Case <>
Date: Wed, 7 Nov 2018 14:50:30 -0500

On Wed, Nov 07, 2018, Hadi Rahmaninejad wrote:
>Du to my long simulation, I need to run my job using GPU instead of CPU.
>However, since I am "using ibelly, I get this error when I run with gpu:
>Implementation does not support Belly options.
> Require ibelly == 0.
>Input errors occurred. Terminating execution."

Could you use restraints (ntr=1) rather than a belly (ibelly=1)?

A "belly" calculation interupts Newton's equations of motion by
artifically setting forces on certain atoms to zero (at one particular
point in the integration scheme.) This can do bad things to thermodynamic
quantities like temperature, pressure, and to other parts of the
integrator (like SHAKE). Having a moving piece of the system in contact
with the fixed piece can lead to imbalances: the behavior (say) of water
around a "rigid" but still fluctuating entity might be different than its
behavior around a completely fixed entity. Further, the implementation in
pmemd doesn't even save you any time.

Basically, there has been little impetus for developers to add this "feature"
to pmemd.cuda. So it is unlikely that this will get added any time soon (but
one never knows, since someone else might want this option as well, and know
how to implement it.)


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Received on Wed Nov 07 2018 - 12:00:03 PST
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