On 3/3/18 9:27 AM, rose rahmani wrote:
Sorry, i can't understand, what do you mean"-zprof0" option? Could you
please give me an example?
Please read the gmx wham help information for a description.
-Justin
On 3 Mar 2018 16:47, "Justin Lemkul" <jalem...@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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