Thanks so much for your explanation, Sir.
Best regards,
Nadafiva
Pada tanggal Kam, 25 Jun 2020 pukul 11.45 Kenneth Huang <
kennethneltharion.gmail.com> menulis:
> Hi,
>
> You can actually use pmemd.cuda for heating/equilibration (I'm not sure
> about minimization). From a workflow POV, it works fine if you don't think
> your system will blow up in heating and have a stable box density volume.
> If it doesn't, you get an error message about the periodic box changing too
> much. In the case it happens, you can just restart till it works, or just
> shift to pmemd till the box volume/density equilibrates out.
>
> Best,
>
> Kenneth
>
> On Wed, Jun 24, 2020 at 9:28 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> > Daer Amber,
> > I heard that pmemd.cuda only use for production step.
> > My question is why pmemd.cuda can not be used for minimization,
> > heating, and equilibration steps in MD?
> > Thank you in advance.
> >
> > Best,
> > Nadaafiva
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Thu Jun 25 2020 - 00:30:03 PDT
