[gmx-users] umbrella windows...

[Justin A. Lemkul]

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 
closest.

> 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

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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