I agree with Dave, my group has been using pmemd.cuda for the entire
equilibration (including initial minimization) of many systems starting
from PDB files and we haven't seen any problems.
On Fri, Oct 27, 2017 at 12:01 PM, David A Case <david.case.rutgers.edu>
wrote:
> 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.
>
> ...dac
>
>
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Received on Fri Oct 27 2017 - 09:30:02 PDT
