Re: box dimension for unwrapped boxes?

From: Aron Broom (
Date: Wed Oct 03 2012 - 10:19:05 CDT

I think that either way is a just a post-processing problem. I think it's
generally better to wrap the coordinates and when making a movie or
something, just keep the peptide centered in each frame. This way the
coordinates for each atom can't become too large (although maybe this isn't
an issue with the binary DCD format).

Anyway, for your problem, I think the box dimensions for re-wrapping are
actually written inside the DCD file, and so there is a convenient method
for wrapping them with VMD. I could be wrong about that, but I suggest
searching through the mailing list, as this problem comes up somewhat


On Wed, Oct 3, 2012 at 11:14 AM, Jacqueline Schmidt <> wrote:

> Dear Namd users,
> I have ran several simulations in NPT ensemble and I did not wrap the
> molecules b/c I wanted to get smooth movement of the peptide (for making
> nice movies from the simulation results). Now I want to get some density
> distributions from some the system species but I have encounterd with the
> problem than I should wrap back the coordinated in order to get the
> distribution plots (I need exact box dimension for that purpose). However,
> since the simulation has been run in NPT, the size of the box changes and
> because I did not wrap the molecucles in the simulation the "measure
> minmax" can not give me the box dimension anymore!!!
> Also in the standard namd output, I can see that the volume is reported
> but not the dimensions in x, y, z
> can anyone please help? can I use these simulations to these density
> distributions??
> looking forward to hearing something positive!!
> thnkas, jackie

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

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