Re: [AMBER] hexagonal unit cell for membrane simulation with NAMD

From: Jason Swails <>
Date: Tue, 12 Nov 2013 19:51:16 -0500

On Tue, Nov 12, 2013 at 6:02 PM, Thomas Evangelidis <>wrote:

> Should I worry about the gaps between the hexagonal shaped boxes in the
> initial configuration of the periodic system? These gaps are filled up
> once the equilibration progresses and the system assumes the shape of the
> unit cell described by the last line of .inpcrd and NAMD parameters
> cellBasisVector1, cellBasisVector2, cellBasisVector3. If these parameters
> were defined correctly would the gaps at the beginning pose a problem?

The only way that the cell changes size or shape is if you're running
constant pressure simulations. It's reasonable (and common) for modeling
programs to create initial boxes that are too large--it's easier to correct
a large box than a small one that forces van der Waals clashes and high

As far as I know, NAMD actually ignores the last line of the inpcrd file
and instead uses the extended system file (but I'm not a NAMD expert).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 12 2013 - 17:00:03 PST
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