is it correct to use the leap frog integrator in GROMACS with WESTPA?

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Ibrahim Mohamed

Sep 3, 2023, 4:06:54 AM9/3/23
to westpa-users
Ii am using GROMACS to perform the dynamics and usually (without using WE) i set integrator = md, tcoupl = Nose-Hoover, and pcoupl = Parrinello-Rahman. However, in the additional tutorials of WESTPA, i noticed that the mdp file contained integrator = sd.
So is it correct to use md as an integrator?


Lillian Chong

Sep 4, 2023, 10:54:08 AM9/4/23

WE simulation requires the use of stochastic dynamics. For MD simulations, this is typically achieved by using a stochastic thermostat, i.e. a Langevin or Bussi's stochastic velocity rescaling thermostat rather than a deterministic thermostat like Nose-Hoover. So you should use the Gromacs settings for either a Langevin or stochastic velocity rescaling thermostat, including the recommended barostat for that thermostat.

For the choice of coupling constant to use with the thermostat, I suggest that you consult this paper by Basconi & Shirts.

All the best,

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Lillian T. Chong, Ph.D.
Professor of Chemistry
University of Pittsburgh
Pronouns: she/her/hers
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