AMBER Archive (2006)

Subject: Re: AMBER: 2-D free energy surface using WHAM

From: David Mobley (dmobley_at_gmail.com)
Date: Mon Jul 03 2006 - 09:33:24 CDT

I think you just want to use two sets of restraints along r and d. For
every umbrella along r, you need to sample all of your umbrellas along
d. That is, think of doing your calculations with a fixed umbrella at
a particular distance d0, and then umbrella sample all r of interest.
Then shift the center d0 to a new center d1, and do the same thing
again.

David

On 7/3/06, Atsutoshi Okabe <okabe_at_cherry.bio.titech.ac.jp> wrote:
>
>
>
>
> Dear all,
>
>
>
> I want to calculate two-dimensional free energy surface along reaction
> coordinate( distances, r and d )
>
> using umbrella sampling and WHAM method .
>
> I could calculate one-dimentional case using these methods, but I don't know
> how to make
>
> Input file on two-dimentional case.
>
> Could you please tell me how to make the input file ?
>
>
>
> Thank you.
>
>
>
> Atsutoshi
>
>
>
>
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