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

[Justin Lemkul]

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

==================================================