The restraints are calculated on the GPU from Amber16 (dihedral),
Amber20(com dihedral). There are a few downloads from GPU to CPU that may
make a slight difference in speed but shouldn't be 3 fold.
To echo .Carlos Simmerling <carlos.simmerling.gmail.com> we will need more
information on your Amber installation, GPU type and how often are you
dumping the dihedral restraint values into your log file.
On Wed, Jan 26, 2022, 4:42 PM Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> 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 Thu Jan 27 2022 - 01:00:03 PST
