[gmx-users] Choosing more PMF-windows

[Shay Teaching]

Ok thanks!

On Sun, Jul 31, 2011 at 5:54 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Shay Teaching wrote:
>
>> Distance of zero between COM of pull_group0 and pull_group1?
>>
>>
> Yes.  The x-axis of the histogram plot indicates the distance along the
> reaction coordinate.
>
> -Justin
>
>  On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Shay Teaching wrote:
>>
>>        Dear GROMACS users,
>>
>>        I have recently completed running several PMF-windows.
>>        After viewing the histrogram file it seems that I need better
>>        sampling at some positions, but the histogram file starts at z=0.
>>        Is there any way to prevent g_wham from starting at 0, and
>>        instead show the real Z-coordinates of the selected-group?
>>
>>
>>    If it starts at zero, then it means your sampling starts at a
>>    distance of zero along the reaction coordinate.  If this is not what
>>    you intended, check your input files.
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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