[gmx-users] umbrella windows...

rama david ramadavidgroup at gmail.com
Fri Jun 1 13:25:59 CEST 2012

Hi Gromacs Friends,

       I am doing Justin-Umbrella sampling tutorial...

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 ..???

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.

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

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

Thank you in Advance...
With Best Wishes,
Rama David
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