that isn't my experience, for a lysozyme test system I get only a few
percent slower when adding dihedral restraints, using pmemd.cuda Amber 20
on 1080TI.
which Amber version are you using, and on which GPU?
On Wed, Jan 26, 2022 at 3:14 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Jan 26, 2022, Richard Kullmann wrote:
> >
> >I am doing regular MD simulations of 4 identical sugar chains. Each of
> >these chains should have the C1-C2-C3-C4 dihedral angle in one of the
> >sugars restrained. The contents of the restraints file are therefore:
> >
> > &rst iat = 3, 18, 16, 13,
> > r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> > rk2 = 32.0, rk3 = 32.0, &end
> > &rst iat = 201, 216, 214, 211,
> > r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> > &end
> > &rst iat = 399, 414, 412, 409,
> > r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> > &end
> > &rst iat = 597, 612, 610, 607,
> > r1 = -58, r2 = -57, r3 = -37, r4 = -36,
> > &end
> >
> >If now run these simulations and compare with simulations without
> >restraints, I get a difference by a factor of 3. The input file is
> >just standard in my opinion:
> >
> > nstlim=250000000,
>
> Given that you think that a quarter of a billion steps is "standard", I'm
> guessing that you are using pmemd.cuda.
>
> I suspect that these restraints are being computed on the CPU. Experts
> on cuda should chime in here.
>
> ....dac
>
>
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Received on Wed Jan 26 2022 - 14:00:03 PST
