[gmx-users] Hamiltonian Replica Exchange

[Thomas Evangelidis]

Thank you all for your comment!

The helix dimer is not very stable and I know that from extensive
accelerated MD simulations I've done with AMBER using various boost values.
Now I want to use a different force field available only in GROMACS, and
though partial solute tempering HREX as the most suitable enhanced sampling
technique considering the available computer resource I have.

I know about the PLUMED implementation of partial tempering scheme. My
question was if I can do the same with GROMACS because the speed with
plumed is significantly impaired compared to serial execution of GROMACS:

3.10 ns/day / Replica with GROMACS 4.6.5 double precision + PLUMED 2.0.2 on
a single node
5 ns/day with GROMACS 4.6.5 double precision on a single node (serial
execution, only one replica)

I don't know if it is the replica exchange scheme that affects the speed so
much, or the "communication" with PLUMED.

On another note, I would like to know you opinion about a couple of ideas I
have:

1) In order to reduce the replicas needed to achieve 30-50% exchange rate
for a given lambda range, I though to selectively heat only the main chain
and CB carbons of the two disordered ends.  Although I don't see anything
wrong with this (except that the system may explode in low lambda
replicas), I would be interested to know the opinion of more experienced
people about possible caveats of the above mentioned rationale.

2) Do you reckon partial solute tempering HREX is suitable to monitor
protein-ligand interactions? In my understanding, ligands will tend to stay
more in touch with "cold" residues of the protein than with "hot" and hence
the results may be misleading. Do you think I should also heat up the
ligands to speed up their diffusion?

thanks,
Thomas



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======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/