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