[gmx-users] Doubt about gmx wham analysis

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

Many Thanks for the swift reply and the help in answering my doubts.

Best Regards,
Bhagyesh  

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, May 31, 2017 6:06:59 PM
Subject: Re: [gmx-users] Doubt about gmx wham analysis

On 5/31/17 8:34 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> In my Protein-ligand system, I have used pull_coord1_dim = Y Y Y and the ligand is pulled along the COM of two groups protein-ligand in all directions to calculate binding affinity using umbrella sampling. On the other hand, the tutorials use pull_coord1_dim = N N Y. Hence, I concluded my reaction coordinate differs as mentioned in the help menu of gmx wham : "If you have some unusual  reaction coordinate you may also generate your own .pdo files and feed them with the -ip option into to gmx wham"
> 

The fact that your reaction coordinate is different from the tutorial is 
irrelevant.  You have an absolutely normal reaction coordinate and does not 
apply to what the gmx wham help text is talking about (which is probably a very 
outdated note at this point, given the massive changes in the pull code in 
recent versions).

> Also, the following warning is thrown by gmx wham: " WARNING, no data point in bin 7 (z=0.403502) ! You may not get a reasonable profile. Check your histograms! "
> I was not sure if the z corresponds to the coordinate axis or just the z-axis (which was not the only reaction coordinate in my system).
> 

It is the length along zeta, the reaction coordinate.  Don't confuse it with the 
z-axis, it's just shorthand.

> All this made me conclude that the pullx files are not enough and the so called pdo files must be necessary, hence the doubt arised. I would appreciate if some more light is shed in this area.
> 

You need better sampling, not archaic file formats.

-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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