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

[Victor Rosas Garcia]

OK.

thank you.  Time to get to work.

Victor

2014-12-14 20:42 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/14/14 9:33 PM, Victor Rosas Garcia wrote:
>>
>> Hello everybody,
>>
>> I'm back.  From the last time I tried this, I took all the
>> configurations (all 500) and did the npt_umbrella equilibration.
>> *Then* I was able to pick evenly spaced configurations (25 of them)
>> and ran the md_umbrella. This is my histogram (g_wham does not
>> complain about poor sampling anywhere):
>>
>>
>> https://drive.google.com/file/d/0B2K7fedV_ZFzRF9qd2FsMTdrSm8/view?usp=sharing
>>
>> and my profile is still wrong
>>
>>
>> https://drive.google.com/file/d/0B2K7fedV_ZFzUTZ6ZW54QXR5a2s/view?usp=sharing
>>
>> Perhaps I need to go up to 31 windows, like in the paper?
>>
>
> Yes, as is stated in the tutorial.  You won't get the same exact profile
> unless you do the same exact procedure.  The profile in the tutorial is
> merely an illustrative example; the tutorial itself is a quick and dirty
> version of the better sampling in the paper, done for didactic reasons.
>
>
> -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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