Umbrella sampling with replica exchange between windows in plumed 2 with gromacs

[Christina]

Hi,
I am trying to figure out whether it is possible to do window replica exchange umbrella sampling with plumed 2.0 and gromacs 4.6.5. If it is possible, it would be great to point me to some tutorial or literature which contain an example of the actual commands that need to be run.
I already performed normal umbrella sampling for my system with plumed and gromacs.
I am very thankful for any advice.
Cheers,
Christina

[Giovanni Bussi]

Hi,

that's covered at the end of this tutorial: http://plumed.github.io/doc-v2.1/user-doc/html/munster.html

Giovanni

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[qingh...@gmail.com]

Dear Prof. Bussi,

I just read the tutorial you mentioned, and I still have one question.

I assume that this is Hamiltonian replica exchange umbrella sampling simulation, but I didn't find a flag of -hrex in the command.
Thus, I am wondering which parts of the Hamiltonian of the system are compared for exchanging replicas, only the restraints potential or the potential of the whole system? Thanks very much!


All the best,
Qinghua

[Giovanni Bussi]

It's not needed since all replicas share the same top file

Giovanni

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[qingh...@gmail.com]

Thanks, Prof. Bussi. I understand it now!

All the best,
Qinghua