&wt
type='DUMPFREQ', istep1=50,
&end
&wt
type='END',
&end
DISANG=disang.120
DUMPAVE=dihedral_120.dat
An example of what I was referring to is shown above. So the DUMPFREQ
allow you to set how often you will print the restraints value during
the simulation.
On Thu, Jan 27, 2022, 7:48 AM Kellon Belfon <kellonbelfon.gmail.com> wrote:
> Hi Richard,
>
> Thank you for the information. Can you also share your prod.in file. The
> log file I refer to is the file you used to print out the restraints value
> using the DUMPAVE option in the MD input file.
>
>
> On Thu, Jan 27, 2022, 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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Received on Thu Jan 27 2022 - 05:30:03 PST
