Hydrogen mass repartitioning and 4-fs time steps in NAMD

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Jul 19 2019 - 11:34:28 CDT

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Hi fellow NAMD users,

Apologies if this seems as spam.

Following up on a question I sent over a year ago to the list, my lab along with that of Yi Wang at CUHK have recently completed a study on the benefits and trade-offs involved with HMR focused on membrane systems using CHARMM force fields. We concluded that HMR and 4-fs time steps are a worthwhile approach, providing almost 2x simulation speed up with just minor effects on system properties. Of course, everyone is encouraged to confirm this for their own systems. If anyone finds a strong counterpoint, I would be interested to see it.

Please take a look at the paper here: https://pubs.acs.org/doi/10.1021/acs.jctc.9b00160

Best,
JC

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