did the run finish? meaning did you complete all of the steps and get
timing info at the bottom of the mdout? if not, then I suggest running
something shorter (maybe 10 minutes or so) so it finishes, and then you can
see how long the Amber job thinks it needed- don't use wallclock time.
compare the reported timings with and without the restraints.
On Thu, Jan 27, 2022 at 4:58 AM Richard Kullmann <
Richard.Kullmann.mpikg.mpg.de> wrote:
> Hello everybody,
>
> thank you very much for your replies. I am indeed using pmemd.cuda. The
> GPUs are NVIDIA GeForce GTX 1080Ti.
> Furthermore, I have been using the AMBER20 installation.
> I am not sure I understand the part about the log file, but I am writing
> to mdout and mdinfo files every 25.000 steps.
> Here is the command I use to run the simulation:
>
> srun pmemd.cuda -O -i prod.in -p top.parm7 -c ../heat/heat3.rst7 -o
> prod.out -r prod.rst7 -x prod.nc -inf prod.mdinfo
>
> Thank you again and best regards,
>
> Richard
>
> On 1/27/22 09:46, Kellon Belfon wrote:
> > 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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> >>>
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Received on Thu Jan 27 2022 - 04:00:02 PST
