[gmx-users] Umbrella sampling

rose rahmani rose.rhmn93 at gmail.com
Sat Mar 3 15:27:27 CET 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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