[gmx-users] Umbrella sampling

[Justin Lemkul]

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" <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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