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

[Victor Rosas Garcia]

Thanks, I'll check it out.  It may be a remnant of a previous, botched, run.



2014-11-18 15:56 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 11/18/14 3:23 PM, Victor Rosas Garcia wrote:
>>
>> 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.
>>
>
> Sampling in window 1 is a little odd - the distribution is incredibly
> narrow, if you can even call it a distribution at all.  Make sure everything
> is OK in that window.  In the absence of a well-defined minimum, you're not
> going to get a sensible profile.  People's mileage varies as far as
> recapitulating that PMF curve, but I have received confirmation from at
> least two other people that the PMF can be reproduced following the method
> in the paper.
>
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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