Re: metadynamics run in NAMD or using plumed in NAMD

From: Rabeta Yeasmin (
Date: Fri Dec 08 2017 - 01:53:49 CST

Thank you so much for your information.
 I am wondering if I can run bias-exchange metadynamics on NAMD with
colvar module as I have found the tutorial for plain metadynamics and
well-tempered metadynamics on NAMD tutorial. For your kind information, I
am trying to find the binding site between a protein and ligand.
And also I am wondering if there is any program to analyze metadynamics
result. I have found one program named META-GUI for analyzing metadynamics
results. But it is based on the output format of plumed. So I am not sure
if I can analyze the metadynamics results from NAMD with its colvar module
over there.

Thanks again.

Rabeta Yeasmin

On Thu, Dec 7, 2017 at 7:22 PM, yjcoshc <> wrote:

> Hi, plumed only officially support NAMD 2.9. For later version I have post
> a patch in plumed user group:
> However I suggest running metadynamics in NAMD with its colvars module.
> Both metadynamics algorithms in colvars and plumed are actually the same,
> but their implementations may differ. The difference includes energy units,
> SIGMA(plumed) vs hillWidth(colvars) and so on.
> 在 2017年12月08日 07:49, Rabeta Yeasmin 写道:
>> Dear NAMD users,
>> I am trying to run metadynamics in NAMD. I have searched online for
>> related information. I have found one tutorial in NAMD tutorial and also
>> found something like-running metadynamics using plumed version- in NAMD
>> version-. I am wondering if these two methods are same or not. If yes, how
>> am I going to use plumed with NAMD.
>> Thanks.
>> Rabeta Yeasmin

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