Re: umbrella sampling by NAMD

From: Jérôme Hénin (
Date: Tue Jun 14 2011 - 07:31:53 CDT

Hi Jafar,

NAMD can do the umbrella sampling simulation, but not the final WHAM
processing. The preferred method is to obtain biased sampling
histograms using NAMD's collective variables with the 'harmonic' and
'histogram' keywords. Then the histograms should be processed into a
PMF with a separate WHAM program. I recommend Alan Grossfield's


On 14 June 2011 13:27, jafar azamat <> wrote:
> Dear NAMD-users,
> I have been simulate a nano tube in water and ion.
> I want to calculate PMF with umbrella sampling method.
> I cannot find a good test file for calculation potential of mea force ions
> with WHAM.
> Can you help me?
> Regards,
>  jafar

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