[gmx-users] Wrong profile obtained in umbrella sampling tutorial

[Victor Rosas Garcia]

Sorry about that Office messup.

These are the new links:
histogram
https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing

profile
https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing

I understand that the profile may not look exactly the same between
different runs, but I do think the difference is large enough to think
something is amiss.

Regards

Victor

2014-11-18 13:14 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 11/18/14 10:58 AM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I have followed Justin Lemkul's tutorial on umbrella sampling, but
>> when I do the data analysis, my energy profile looks wrong.
>>
>> Please see the profile:
>>
>>
>> https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/profile.png
>>
>> and the histogram:
>>
>>
>> https://uanledu-my.sharepoint.com/personal/victor_rosasgr_uanl_edu_mx/Documents/Shared%20with%20Everyone/histo.png
>>
>> I would be grateful on any pointers about how to start diagnosing what
>> is wrong.  I am using Gromacs 4.5.4 under linux.
>>
>
> Please post your images somewhere public that does not require Office365
> credentials.
>
> Note that the tutorial will not *exactly* reproduce the PMF profile, since I
> used a slightly different window setup to produce it (described in the paper
> referenced in the tutorial).
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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