[gmx-users] Pressure coupling in expanded ensemble simulations
Gregory Man Kai Poon
gpoon at gsu.edu
Fri May 17 16:06:30 CEST 2019
I am just following up on your thoughts on how carrying out expanded ensemble at NVT and converting back to NPT on the mailing list. Again I appreciate your advice in this area.
On 5/8/2019 12:01 PM, Michael Shirts wrote:
Yeah, this is an unfortunately place in the code where not all combinations
work - very long story. Hopefully this will be working better in 2020.
What I would recommend is, if possible, performing the expanded ensemble
simulation at NVT. Everything should work fine there (paper coming out
hopefully soon comparing a bunch of free energy methods). Once can always
correct the free energy at lambda=1 from NVT to NPT. I Can fill in the
You do NOT want to do Berendsen for NPT when running expanded ensemble.
The results will be incorrect (as I have learned by sad experience_
On Wed, May 8, 2019 at 8:14 AM Gregory Man Kai Poon <gpoon at gsu.edu><mailto:gpoon at gsu.edu> wrote:
We are interested to do expanded ensemble simulations (such as simulated
tempering) on GROMACS. Extensive fiddling with the settings and
googling on other people's experience suggests that these simulations
must use the md-vv integrator, which in turn is compatible with
Berendsen or MTTK coupling for pressure. However, MTTK does not work
with constraints, which are needed for the forcefields. Berendsen can
handle constraints but is not recommended for preserving thermodynamic
ensembles. Any ideas on how one should proceed?
Many thanks for your thoughts.
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Gregory M. K. Poon, PhD, RPh
Departments of Chemistry and Nutrition | Georgia State University
NSC 414/415/416 | 50 Decatur St. SE, Atlanta, GA 30302
P.O. Box 3965 | Atlanta, GA 30303
Ph (404) 413-5491 | gpoon at gsu.edu<mailto:gpoon at gsu.edu>
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