RE: Hamiltonian Replica exchange configuration file

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Aug 29 2019 - 17:47:54 CDT

Hi Neha,

I've done this for replica exchange TI. The trick is modifying what part of the energy term NAMD looks for when determining the energy difference and dealing with the bookkeeping for what exchanges mean. What part of the hamiltonian were you hoping to exchange across?

-Josh

On 2019-08-29 15:05:27-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hello,
I am trying to run a Hamiltonian replica exchange MD using NAMD. I was successful in running umbrella sampling Replica exchange MD tutorial. But unfortunately, I am not able to adapt the umbrella.namd for H-REMD. Could you please share a configuration file that can successfully run an H-REMD simulation?
Best regards,
Neha

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