[gmx-users] Periodicity in umbrella sampling
busato.matteo at spes.uniud.it
Mon Mar 26 12:21:32 CEST 2018
Hi to everyone,
I am performing an umbrella sampling simulation of an ion pulled through a biphasic system. The box is 3.6 X 3.6 X 7.3 nm and the ion has been pulled along the z-axys for about 3 nm.
In Justin Lemkul's tutorial about umbrella sampling (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/02_define_box.html) I've read that "one must allow enough space in the pulling direction to allow for a continuous pull without interacting with the periodic images of the system".
This turns into the fact that the pulling distance must always be less than half the box size in the pulling direction, but what about the other two directions? In my case, if I put no restraints on the x and y-axes movements of my ion, it will probably interact with the periodic images of the box in the x and y directions (e.g. go out from a box surface and get in by the other side).
Could this affect the final PMF result?
Thank you in advance for your answer.
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