Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

Mohsen Ramezanpour ramezanpour.mohsen at gmail.com
Wed Jul 31 16:19:20 CEST 2013

Dear Dr.Justin

I read that article, It was very helpful. Thanks a lot.
After using g_wham with bootstrapping options.
I have got an averaged PMF profile (like Fig.2C in that article) and
an standard deviation (like Fig.2D In that article) which obtained in
this way.
As you see, the standard deviation is equal to zero at Z=1.5 nm
(because I defined all PMFs as Zero at that point) and it is around 2
kj/mol in Z=0.25

Since I am interested to Gibbs Binding Free Energy(GBFE) (the
difference between the Gibbs energy of these points, Z=.0.25 &1.5 nm),
Is it right to say the error for estimating of GBFE is 2 kj/mol ?

Thanks in advance

On 7/31/13, Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com> wrote:
> Thank you for your reply Dr. Justin
> On 7/31/13, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 7/31/13 7:00 AM, Mohsen Ramezanpour wrote:
>>> Hi everyone
>>> How can we have an error estimation for Gibbs binding free energy when
>>> I do umbrella sampling and PMF profile?
>>> Actually I did an umbrella sampling for protein and ligand complex and
>>> I have a PMF profile now but I do not know how much is my error!
>> Read g_wham -h and the associated g_wham paper referenced in the Gromacs
>> manual.
>>   It explains everything.
>> -Justin
>> --
>> ==================================================
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> ==================================================
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