[gmx-users] Umbrella Sampling Tutorial Question

Justin Lemkul jalemkul at vt.edu
Sat Nov 1 01:52:06 CET 2014

On 10/31/14 8:48 PM, Agnivo Gosai wrote:
> Dear Users
> Firstly thanks to Dr. Lemkul for his immensely informative and helpful
> tutorials. I am following the umbrella sampling tutorial for one of my
> projects.
> During the placement of the molecule inside the box , the tutorial tells us
> to visualize in VMD. Now , upon visualizing I find that the 4 strands of
> protofibril protein look separated.
> Then we are to restrain one of the strands and pull the next stand in the
> pulling simulation.
> I can not understand how this is physically possible as the strands
> "appear" to be "physically separated" and we proceed to calculate PMF based
> on binding energy.
> Kindly shed some light on this issue , please. Pardon for my ignorance.

The strands shouldn't be separated.  The input .pdb file is a pentamer.  The 
commands in the tutorial won't modify the coordinates.  If you're seeing 
something significantly different from the image in the tutorial, start over and 
don't do anything that isn't explicitly stated in the tutorial.  If you're still 
having issues, you're going to have to link an image so we can see what is going 
on.  The phrase "look separated" isn't very descriptive.



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


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