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HanatoK / Apoa1-Benchmark

Apoa1 benchmark for NAMD, AMBER, GROMACS and openMM
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margin in apoa1_nvt.namd #2

Closed songyongshun closed 1 year ago

songyongshun commented 1 year ago

the margin is set to 8, which give a warning: Warning: MARGIN IS UNUSUALLY LARGE AND WILL LOWER PERFORMANCE I change it to 0, and the performance is doubled. I also checked the parameter in official package as find in https://www.ks.uiuc.edu/Research/namd/utilities/. They also have a margin of 0, though the force field is Charmm22.

HanatoK commented 1 year ago

@songyongshun In NAMD 3.0 alpha, it was suggested to set to 4 (see https://www.ks.uiuc.edu/Research/namd/alpha/3.0alpha/), but in a longer simulation time I still got error of margin violation as I remember (these benchmarks were uploaded a few years ago).

songyongshun commented 1 year ago

I tested it with namd2.13, maybe the differece comes from the different versions. I didn't notice the suggested margin value until you pointed it out. Thanks a lot.🙂