Re: Hamiltonian Replica exchange configuration file

From: neha rana (neha2009rana_at_gmail.com)
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.

-Neha

On Thu, Aug 29, 2019 at 6:47 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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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