Re: [AMBER] Use of pmemd for minimisation and equilibration

From: David A Case <>
Date: Fri, 27 Oct 2017 12:01:35 -0400

On Fri, Oct 27, 2017, David Case wrote:
> > I was wondering if it is okay to run minimisation and equlibration steps
> > using pmemd.cuda.
> Sure--I do that all the time....dac

Let me expand: if you have a bad starting structure, then doing the
initial minimizaton on a CPU may be required. But you will see that an
attempted CUDA run failed in that case.

But for simulations that start (say) from an X-ray structure in the PDB, I
haven't seen reasons not to use pmemd.cuda for everything.


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Received on Fri Oct 27 2017 - 09:30:02 PDT
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