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

Juan José Galano Frutos juanjogf at gmail.com
Wed Feb 15 17:23:24 CET 2017

Thanks Mark for your replay.

About the part where you say...

>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

...yes, I agree with you that one must be aware about this issue. But about
the other aspect you pointed out:

>or if you're using PME, so that everything
>sees everything at long range

...I'm not so clear.

The point is we've used PME both in the original simulations and in the 'rerun'
ones (the .mdp files are almost idem). Then, what should we do here to
avoid this
problem? ...maybe to turn off the PME long-range electrostatics only
in the rerun
step? If so, wouldn't that importantly change results in terms of
Energy only by
the effect of changing the electrostatic treatment?
Another solution? ...maybe setting up a different electrostatics from
the begining
(the same both in the original simulations and in the rerun ones)?
What's treatment
we could use to get the longe-range electrostatics turned off without
loosing so
much accuracy in terms of Energy? ...'cut-off', 'PME-Switch' maybe? ... or a
coulomb-modifier such as Potential-shift-Verlet?

Any suggestion there, please?

Thanks a lot.


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)

More information about the gromacs.org_gmx-users mailing list