Re: how to calculate the box size

From: Aron Broom (
Date: Tue Mar 06 2012 - 08:44:57 CST

What if for the water molecules in your system you calculate from the
center of mass of the waters rather than just the atomic coordinates? I
don't know what the real answer is, but that would shrink your box ever so

On Tue, Mar 6, 2012 at 2:48 AM, mjyang <> wrote:

> Dear NAMD users,
> I performed a simulation by NAMD for a protein system solvated by a
> cubic water box. Now I extracted the snapshots from NAMD trajectory for
> postpone analysis, in which the protein should be centered in the box. The
> box size was calculated by (max_x-min_x, max_y-min_y, max_z-min_z), where
> max_x,y,z and min_x, y, z are the maximum and minimum coordinate values of
> the extracted frame. However, the box size calculated in this way is a
> little larger than the real one, resulting in gaps in the recentered box.
> It seems that the box size written out by NAMD in the *.xsc file is better
> than what I calculated. But the NAMD output size (in *.xsc file) only
> corresponds to the last frame of a segment of trajectory file and I need
> the size for each frame in the traj. Could someone please tell me how NAMD
> calculate the box along MD simulations?
> Many thanks.
> Mingjun

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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