[gmx-users] bilayer leaflets separating
David van der Spoel
spoel at xray.bmc.uu.se
Mon Nov 15 09:26:58 CET 2004
On Sun, 2004-11-14 at 16:35 -0600, eric jakobsson wrote:
> 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.
Is this even when you turn on the pressure correction for the cut-off?
(dispcorr = enerpres)
I would think it would be mainly pressure related.
> 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
> >gmx-users mailing list
> >gmx-users at gromacs.org
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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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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