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
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
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
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
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
