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 - 02:00:02 PST
