[gmx-users] Pressure coupling in expanded ensemble simulations
Gregory Man Kai Poon
gpoon at gsu.edu
Mon May 20 14:32:22 CEST 2019
Hi Michael,
Our system of interest here is a set of small proteins with disordered regions. The literature suggests that RE methods are not well-suited to sampling such systems with dynamically "hot/cold" regions (and requiring more specialized techniques such as the link below) on the one hand, while approaches such as simulated tempering may be more efficient on the other. We also wanted lower requirements on CPU cores given the level of hardware we have access to.
https://www.ncbi.nlm.nih.gov/pubmed/25136274
We have been working with toy systems such as the Ala10 peptide in TIP3P to define the workflow with Metropolis MC moves and the WL histogram. As you suggested previously, we ran an NVT ensemble from 280 to 330 K, with 11 linearly spaced intervals (with a v-rescale tcoupl), starting with a NPT-equilibrated system. The usual diagnostics look okay (e.g., acceptance ratio). The pressure of the system after several hundred ns runs did not seem very different, given the typical RMSD on the order of 100's of bar even when pressure coupling is on. Obviously, if we could move the sampling back to NPT would be very helpful. Kindly let me know what specific info you would like to see.
Thanks again for your help,
Gregory
On 5/19/2019 11:05 PM, Michael Shirts wrote:
Ah, sorry, I thought there was more information coming.
Have you considered just using temperature replica exchange? It's not that
much less efficient, and is easier to deal with. Replica exchange should
be working with NPT (as long as you use Parrinello-Rahman and a reasonable
temperature control algorithm). The size scaling is about the same; i.e.
if you need a lot of replicas, you will also need a lot of expanded
ensemble intermediates.
On Fri, May 17, 2019 at 8:06 AM Gregory Man Kai Poon <gpoon at gsu.edu><mailto:gpoon at gsu.edu> wrote:
Hi Michael,
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.
Best wishes,
Gregory
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
details.
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>
<mailto:gpoon at gsu.edu><mailto:gpoon at gsu.edu> wrote:
Hi all:
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.
Gregory
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Gregory M. K. Poon, PhD, RPh
Associate Professor
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><mailto:gpoon at gsu.edu><mailto:gpoon at gsu.edu>
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Gregory M. K. Poon, PhD, RPh
Associate Professor
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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