[gmx-users] bilayer leaflets separating

eric jakobsson jake at ncsa.uiuc.edu
Sun Nov 14 23:35:19 CET 2004

Some time ago we did liquid hexane simulations and found that using 10 
angstrom LJ cutoff, the liquid evaporated---analogous to the leaflets 
separating.  It did not happen with 15 angstroms, but we had to go to 20 
angstroms before the density leveled off. So we believe that 10 angstroms 
is too short for the LJ cutoff, and we always use 20 angstroms. This seems 
at first surprising, since LJ falls off as the 6th power, but in contrast 
to the Coulomb potential there is no shielding by opposite charges---all 
the the long range LJ is attractive.

Hope this is helpful,

At 09:03 PM 11/11/2004, you wrote:
>I am experiencing something very strange: the leaflets of my bilayer
>are continuosly separating, thus creating a large gap in the middle of
>the bilayer. I ran the simulation for 100 ps and the gap was about 10
>nm. I tried this same simulation many times, in several machines, and
>I cannot get it to be stable. Would anyone have any idea what may be
>the problem? This is a simulation for a small bilayer with 64 and 3846
>water molecules (from Tieleman's webiste). The simulation are in the
>NPT ensemble (1 bar and 323 K), with 1.0 nm and 1.8 nm cut-off for the
>LJ and eletrostatic interactions, respectively. Periodic conditions in
>all directions. The initial velocity were generated at the start of
>the simulation. I am using the GROMOS forcefile for the lipid and SPC
>water. The strangest thing is that I can use this same forcefield and
>conditions for the simulation of a large bilayer (128) and I do not
>encounter this problem. I would greatly appreciate input/comments.
>                 --Amadeu
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Eric Jakobsson, Ph.D.
Professor, Molecular and Integrative Physiology, Biophysics and 
Computational Biology, Beckman Institute, Bioengineering, Biochemistry, and 
Senior Research Scientist, National Center for Supercomputing Applications
4021 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue
Urbana, IL 61801
ph 217-244-2896
fax 217-244-2909
e-mail jake at ncsa.uiuc.edu

(Since May 2003 I have been on leave from the University of Illinois to 
serve as the Chair of the NIH Biomedical Information Science and Technology 
Consortium and the NIGMS Center for Bioinformatics and Computational 
Biology, in Bethesda, Maryland.  However I commute to Urbana almost every 
week to maintain my research lab here. 

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