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

Mark Abraham mark.j.abraham at gmail.com
Wed Feb 15 15:30:46 CET 2017


The energies are well defined, either way. (Whether they'll be useful is
another matter...) The problem comes when one side of your shell can see
the other across the gap within the cutoff, and you're still thinking of it
as an isolated single shell. Of if you're using PME, so that everything
sees everything at long range. Using no PBC and infinite cutoff is at least
cleanly defined (but not yet implemented in the Verlet scheme).


On Wed, Feb 15, 2017 at 2:36 PM Juan José Galano Frutos <juanjogf at gmail.com>

> 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 <+34%20976%2076%2028%2006>
> Institute for Biocomputation and
> Physics of Complex Systems (BIFI)
> Mariano Esquillor, Edificio I + D - 50018
> Zaragoza (Spain)
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