[gmx-users] Selecting box dimension and COM position - Pull Code

Agnivo Gosai agnivogromacs14 at gmail.com
Sun Oct 26 20:43:22 CET 2014

Dear Users

I have gone through the tutorial on umbrella sampling by Dr. Lemkul and am
using the methodology described therein for running my own simulations.

It is explained that :-
"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."

Are there any guidelines for assigning the COM position of my biomolecule
complex and the x,y,z dimensions of my simulation box keeping in mind the
above explanation.
Or I should go about it in a trial and error basis?

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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