[gmx-users] genion deletion edges

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 22 11:32:36 CET 2004

On Mon, 2004-11-22 at 03:25 -0500, dsh2002 at med.cornell.edu wrote:
> Hello All,
> My system consists of POPC bilayer, solvent water above and below the
> membrane and a peptide in the membrane.
> I took the POPC patch from a previously equilibrated Larger patch
> originally from Tieleman, that has been simulated for some time.  So my
> patch does not have very clean edges, meaning some parts of some lipids
> protrude out of my boundaries for the box.  Will increasing the box
> dimensions so that all of the lipids totally fit in the box mess up the
> simulation by decreasing the density of the bilayer?  And does protruding
> lipids or atoms mess up the periodic boundary conditions?
> I noticed when I used genion to add Cl's to my system, the coordinate file
>  seemed to "clean" up the edges of my box by truncating ends of lipids. 
> Is this a weird artifact that I have made or is this a general process of
> genion?
Doesn't genion just put it back in the box?
> any insights would be much appreciated.
> danny.
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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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