[gmx-users] How treat PBC with -rerun option when simulate protein in a defined water shell?

[Juan José Galano Frutos]

Hi there,

We are doing simulation in which we are interested in studying Energies,
Enthalpies, etc. changes in systems with increasingly water shells around a
protein. In this sense, we first extract bulk waters in order to leave the
mentioned water shells with a defined radius around the protein. Then we do
a rerun in order to recalculate the system energies, but my doubt here is:
what exactly to do with PBC in the .mdp file? My doubts here come up
because the system now (protein + water shell) is not a geometric box like
a dodecahedron or a cubic box, and I am afraid about whether the energies I
am obtaining are totally wrong. Do you think it will be better here not to
use PBC or you think there is no matter in doing the rerun keeping PBC on?
I guess that keeping PBC on, there will be some empty space between each
side box (the space left by water removed), so I feel it could be important
...

Thank you very much.


Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)