Re: Hamiltonian Replica Exchange MD in NAMD

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Jan 18 2018 - 18:02:37 CST

You might also find the tutorial “Methods for calculating Potentials of Mean Force” helpful.

Best,
JC

> On Jan 18, 2018, at 5:14 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:
>
> 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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