Re: Hamiltonian Replica exchange configuration file

From: neha rana (
Date: Thu Aug 29 2019 - 18:18:09 CDT

Thanks for your prompt reply Josh.
I am not aware how you can do that. I have noticed that umbrella.namd
stores a POTENTIAL array. Is that what you're referring to? So my objective
is that I have a couple of protein-ligand models (same system) with some
conformational differences. I want to explore the local conformational
space of this system by using those models as replicas at the same
temperature and exchanging only the potential part of their hamiltonians.


On Thu, Aug 29, 2019 at 6:47 PM Vermaas, Joshua <>

> 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 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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