[gmx-users] Inverting PBC for membrane simulations

Alan Dodd anoddlad at yahoo.com
Wed Dec 15 16:07:56 CET 2004

I have considered modelling a neighbouring cell
explicitly as you say, it's just that the simulation
doubles in size to reduce the chances of the peptides'
effects on the bilayer influencing each other, and I
was hoping to find a computationally cheaper way.

I'm not sure what you mean by being unable to tell
what the ensemble is - can you explain?

Alan Dodd
University of Bristol

Tue Dec 14 03:26:32 CET 2004
I think it is a better idea to set up the simulation
such that the two 
leaflets are chemically the same, so they have a
chance to have the same 
surface tension.  For example, if you have a protein
in one leaflet, you 
should also have it in the other leaflet.  Otherwise,
you just don't know 
what your ensemble is.

At 05:15 AM 12/13/2004 -0800, you wrote:
>As there is a potential surface tension difference
>between the two leaflets of the bilayer in my
>simulation,  I would like to be able to modify the
>periodic boundary conditions such that the z axis is
>inverted in the xy neighboring cells (by rotating
>about the xy diagonal) - so a lipid can diffuse out
>the top leaflet and into the bottom leaflet at the
>edges of the box.  I know of an example where similar
>things have been done before, but not with Gromacs.
>Are there any ways in which this can be done?
>Alan Dodd
>University of Bristol
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative
Physiology, and of 
Senior Research Scientist, National Center for
Supercomputing Applications
Professor, Beckman Institute for Advanced Science and
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of
Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for
Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical
Information Science 
and Technology Initiative Consortium, but maintaining
my research lab at 
Illinois by periodic commuting.  My usual schedule is
four days a week at 
NIH and three days a week at Illinois.)

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