[gmx-users] Inverting PBC for membrane simulations
jake at ncsa.uiuc.edu
Thu Dec 16 05:57:16 CET 2004
Re your first point---yes, the simulation is twice the size, but you get
twice the conformational sampling, so the only extra computational cost is
in equilibration. After that, you need only run half as long to get the
same amount of conformational sampling, because the equilibrated system is
Re your second point: The computation of the surface tension depends on
integrating the virial component in the membrane plane along the entire
distance normal to the membrane. If the sum of the lateral virials is
different in the two leaflets, which it certainly will be if they do not
have the same number of the same types of molecules, then the entire system
does not have a single well-defined surface tension.
At 07:07 AM 12/15/2004 -0800, you wrote:
>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?
>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
>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
>Computational Biology and Chair of the NIH Biomedical
>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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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 Technology
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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