[gmx-users] umbrella windows...

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 1 13:31:47 CEST 2012

On 6/1/12 7:25 AM, rama david wrote:
> Hi Gromacs Friends,
>         I am doing Justin-Umbrella sampling tutorial...
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html
> After pulling I found the Chain A is moving away from protofibril but reaches
> up to the other end of the cell..
> So Is these situation Satisfy the Minimum image condition??? or Am I doing some
> wrong ..???

If you set up the box properly, there should be no minimum image violation, nor 
is it particularly relevant here.  Chain A doesn't see itself and it is several 
nm away from any other protein molecule, regardless of which periodic image is 

> as tutorial Says..
> GROMACS calculates distances while simultaneously taking periodicity into
> account. This, if you have a 10-nm box, and you pull over a distance greater
> than 5.0 nm, the periodic distance becomes the reference distance for the
> pulling, and this distance is actually less than 5.0 nm! This fact will
> significantly affect results, since the distance you *think* you are pulling is
> not what is *actually* calculated.

This statement is not related to the minimum image convention, it is addressing 
a limitation in the pull code algorithm.

> My Query is on  very basic concept...
>   tutorial says....
> In this example, we will be sampling COM distances from 0.5 - 5.0 nm along the
> z-axis using roughly 0.2-nm spacing. The following example commands may or may
> not be literally correct (the frame numbers may differ), but will serve as an
> example as to how to run grompp on separate coordinate files to generate all 23
> inputs (note as well that 23 is the amount of windows required to obtain 0.2-nm
> spacing over roughly 4.5 nm;
> my summary_distances.dat has following lines..
> 0    0.5011713
> 1    0.5068762
> 2    0.4948514
> ..
> .
> .
> 160    0.6993698
> so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it right???

Seems reasonable.  The tutorial tells you to pick intervals of about 0.2 nm.

> I choose total 28 windows instead of 23 ...So is it good or bad ???

It is unnecessary.  You'll be covering extra space that winds up just wasting 
time.  The PMF will level off long before the 5.0 nm of COM separation, which in 
itself is overkill.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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