[gmx-developers] PBC with p2sub1 from pbc_dx() modifications

hessb at mpip-mainz.mpg.de hessb at mpip-mainz.mpg.de
Tue May 30 20:59:07 CEST 2006

> I intend to model a membrane using P2sub1(-x,y+1/2,-z) PBC as in Dolan,
> Venable,
> Pastor, and Brooks Biophys. J. Vol. 82 May 2002, 2313-2325. This requires
> a
> modified PBC such that lipids exiting the box from the upper leaflet enter
> the
> box in the lower leaflet of the membrane.
> Do I need to do anything other than make the appropriate changes in
> pbc_dx() in
> src/gmxlib/pbc.c? i.e. will this take care of things like the nonbonded
> list,
> PME, pressure scaling, etc.?

Several years ago I had thought of implementing this,
but I thought I was too much work.

pbc_dx is (almost) not used at all during normal simulations in Gromacs.
pbc for non-bonded interactions is handled by the grid neighbor search,
there one would have to change the shifts of the i-particles,
but I wouldn't know of an elegant way to fix the shift forces
used in the pressure calculation.
The bonded interactions are handled by the graph code.
This graph can be circumvented by using pbc=full
in which case pbc_dx is used for bonded interactions.


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