Also, try cut=9
What water model are you using ?
On 11/4/25 11:33 AM, Carlos Simmerling via AMBER wrote:
> [External Email]
>
> - switch to the MC barostat (barostat=2)
> - use H mass repartitioning and a dt=0.004
>
>
> On Tue, Nov 4, 2025 at 11:13 AM Daniel Hall via AMBER <amber.ambermd.org>
> wrote:
>
>> Hello amber community,
>>
>> I hope everyone is well.
>>
>> I am experiencing a poorer than expected performance when running explicit
>> solvated system, with performances ~330 ns/day for a system of size ~18k
>> atoms using amber24 on an Ubuntu 24.02 system. Here is my workstation
>> hardware;
>>
>> CPU: Intel Xeon W-2295, 18 cores @ 3 GHz
>> GPU: NVIDIA GeForce RTX 3080 10GB
>> Storage: 1 TB M.2 2280 PCIe NVMe Gen4x4 + 2 TB M.2 2280 PCIe NVMe Gen4x4
>> RAM: 64GB (4 x 16GB) DDR4 2933 MHz
>> PSU: 1000W
>>
>> This is the prod.in using pmemd.cuda;
>>
>> igb = 0, imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 10.0, ntr = 0,
>> ntc = 2, ntf = 2,
>> tempi = 300.0, temp0 = 300.0,
>> ntt = 3, gamma_ln = 2.0,
>> nstlim = 250000000, dt = 0.002,
>> ntpr = 50000, ntwx = 50000, ntwr = 50000,
>> tol = 0.00001
>> /
>>
>> Troubleshooting I’ve already performed;
>>
>> * I have checked that the GPU is being utilized, although the memory
>> usage is only 472 Mb. Both the NVIDIA drivers (580.95.05) and CUDA versions
>> (13.0) are up-to-date, and the correct version of CUDA is being used.
>> * The GPU is in the correct PCIe slot, x16 gen 3, and is forced x16
>> speed in the BIOS.
>> * The GPU isn’t thermal throttling, as it doesn’t exceed 75 °C.
>> * The maximum power performance option is selected by the workstation.
>> * The simulation is being in single-precision and not double-precision.
>> * I would normally use 5000 for ntpr, ntwx and ntwr but increasing to
>> 50000 did not make a difference.
>> * Utilising more CPU cores made performances worse.
>>
>> Is there anything else that I have missed or could do to improve
>> simulation performance.
>>
>> Any suggestions are greatly appreciated 😊
>>
>>
>> Regards
>> Dan.
>>
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--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Nov 04 2025 - 09:00:04 PST
