On 06/01/2025 19:13, Kiriko Terai via AMBER wrote:
> Hello,
> I have recently been attempting to simulate a multi-heme protein system in explicit solvent OPC at temperatures 275, 300, 325, 350, and 375 K. I have prepared .prmtop and .inpcrd files. I am currently going through minimization and relaxation steps following the protocol here: https://ambermd.org/tutorials/basic/tutorial13/index.php#Files_
> I can minimize my system, heat the system from 100 K up to the target temperature, run constrained NVT/NPT equilibration, and relax the system by gradually decreasing the restraints. But when I check the relaxation using cpptraj and analyze the temperature, density, volume, and etc., I find obvious temperature spikes in the Temperature.agr plot. I do not see any issues with Density.agr and Volume.agr.
> To fix this issue, I have tried running the relaxation for longer times, running the 2mdheat.in step with smaller time steps (1fs vs 0.5fs), and running the relaxation steps with more gradual decrease of restraint_wt. In the manual, restraint_wt changes from 100, 10, 0.1 and to 0. Instead, I changed from 100, 50, 10, 0.1 and to 0. However, the temperature spikes are still present.
> Any help would be much appreciated. Below are my input files for the minimization and relaxation steps for target temperature 375K. I also attach the Temperature.agr that shows the temperature spikes.
> Thank you,
> Kiriko
Hi Kiriko,
question: are you running the simulation with PMEMD or with Sander? And, are you running it on CPU or on GPU?
I'm asking because of this
http://archive.ambermd.org/202404/0077.html
As you see, I've reported exactly this kind of problem long ago, but in the end no conclusion was reached about it. Note that, in my case, the problem appears only when using PMEMD on CPUs. If using
GPUs, or if using Sander, all seems fine.
I look forward to your answer!
Cheers,
Charo
--
Dr. Charo I. del Genio
Institute of Smart Agriculture for Safe and Functional Foods and Supplements
Trakia University
Stara Zagora 6000
Bulgaria
https://charodelgenio.weebly.com
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Received on Mon Jan 06 2025 - 09:30:03 PST
