[AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Fri, 8 Nov 2013 02:37:19 +0200

Dear list,

Does anyone know if I can create a hexagonal membrane patch with lipid11 ff
to run a simulation in a hexagonal unit cell with NAMD? CHARMM-GUI provides
an option to create a hexagonal box but I think in the .prmtop file there
is a pointer named "IFBOX" which determines the box size, and since AMBER
does not support that kind of shape I suspect there might be a conflict
with the cell basis vectors in the NAMD configuration file. The same may
apply with the lattice vectors written in the last line of .inpcrd.

Other than that, the lipid11 tutorial states that I should choose a
Rectangular box type in CHARMM-GUI since this geometry is required for
constant surface tension. Will there be a problem if I choose a Hexagonal
box type and run the simulation in NAMD provided that I define correctly
the cell basis vectors?

Could anyone please clarify these points?


Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Nov 07 2013 - 17:00:03 PST
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