Re: Hamiltonian Replica Exchange MD in NAMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Thu Jan 18 2018 - 16:14:04 CST

Hi Youngwoo,

See "A Tutorial on One-dimensional Replica-exchange Umbrella Sampling"
under http://www.ks.uiuc.edu/Training/Tutorials/. There are about a
half-dozen different ways to call exchanging your applied bias
(including Hamiltonian Replica Exchange), but Replica Exchange Umbrella
Sampling is the oldest terminology. Unfortunately, the tutorial is in
some ways a bit dated (compiling VMD isn't strictly speaking needed
anymore since at least 2.11 I think), however the scripts themselves are
the backbone for most of the REUS work done in NAMD.

-Josh

On 01/18/2018 03:07 PM, Youngwoo Woo wrote:
> Dear, NAMD users
>
> I'd like to start a Hamiltonian Replica Exchange Molecular Dynamics
> simulation in NAMD.
> I've looked for both the tutorials and questions in NAMD tutorials
> page and user guide however, I could not find any source to get into.
> Could anyone send me tutorial file or a link or a simple configuration
> file that I can follow?
>
> Sincerely,
>
> Youngwoo

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