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

[Victor Rosas Garcia]

OK Justin, thank you for your patience.  I'll do as you say.

Have a Happy New Year!

Victor

2015-01-07 10:50 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 1/6/15 2:04 PM, Victor Rosas Garcia wrote:
>>
>> 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?
>>
>
> Since this has been going on for a while, I may be forgetting details - are
> you following *exactly* the procedure from the paper?  As I said before, you
> won't reproduce the PMF profile using the tutorial; only by doing what is in
> the paper should you expect to reproduce it.  Pulling directly on the NMR
> pentamer does lead to an artificially low barrier because the side-chain
> packing leaves several voids that decrease peptide-peptide affinity.  So, if
> you run 100 ns unrestrained MD, then do SMD and subsequently umbrella
> sampling, you should be able to reproduce what's shown in the tutorial.
>
> -Justin
>
>
>> 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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>
>
> --
> ==================================================
>
> 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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> Gromacs Users mailing list
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