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

[Victor Rosas Garcia]

Hello everybody,

I'm back from the holidays.  Still working on the PMF tutorial.

Perhaps I'm just dense.  These are the results of the latest run (34
windows, wham complains of poor sampling around 5.57 nm)

The histogram is at:
https://drive.google.com/file/d/0B2K7fedV_ZFzSUpsOGVOY01mc00/view?usp=sharing

and the resulting (wrong) profile

https://drive.google.com/file/d/0B2K7fedV_ZFzWFB1TURoanB4U2c/view?usp=sharing

Any suggestions?

Victor

2014-12-15 7:24 GMT-06:00 Victor Rosas Garcia <rosas.victor at gmail.com>:
> 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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