[gmx-users] Umbrella sampling

[rose rahmani]

Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?

On 3 Mar 2018 16:47, "Justin Lemkul" <jalemkul at vt.edu> wrote:



On 3/3/18 7:02 AM, rose rahmani wrote:

> Hi
>
> I use umbrella sampling to calculate PMF, for studying the interaction of
> different aminoacids with nanosheet separately. But at the minimum distance
> from sheet, potential is zero for all PMF diagrams. I mean there isn't any
> positive potential even at closest distance of aminoacid from sheet. I did
> pulling and sampling manyyy times with different rates ...,still the same
> problem... how could it be possible?What is the problem? I really get
> confused. There isn't any closer distance to sample it.
> Would you please help me?
>

WHAM works by assigning the leftmost (lowest index) window a free energy
value of zero, and then constructs the rest of the profile relative to it.
You can adjust this with the -zprof0 option.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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