[gmx-users] lipid solvent

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 16 06:26:16 CEST 2007


> The lipids aggregated and surround the protein (as expected) but
> asymetricaly in the box.

What do you mean with this? Did you consider PBC? Try centering your
system using  the protein for the center of mass.

> I have selected only the lipids from the last run
> at a maximum distance of 20 A from the protein.
> my problem is that my system is now circular (due to the lipid selection
> method) and I want to put it in a new box
> without adding more lipid or water but there will be no lipids in the
> box corners.
> Is there an easy way to solve this (the is no circular boxes and I have
> some problems using dodecahedron ones)?

You could define a hexagonal prism, which is as close as you can get
to a cylinder.

Hope it helps,


Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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