Re: [AMBER] NVT equilibration crash using CUDA

From: Jason Swails <>
Date: Tue, 10 Jun 2014 08:10:03 -0400

On Tue, 2014-06-10 at 13:36 +0400, James Starlight wrote:
> one question about solvent dynamics seen in the npt production run
> initially using octahedral cell. During visualization by VMD I've seen
> water spreading in all dimensions with significant increasing of the box
> size (looks like no pbs have been applied). From tutorial I've found
> possible re-imaging script using cpptraj after which my system looks like
> in the fixed box size. Does such system increasing is some artifact?

It is an imaging artifact. If you set "iwrap=1" in the mdin file it
will enable wrapping in the output coordinates.

> How
> I could measure pbc box vectors during md ?

The volume of the unit cell should be printed in the mdout file every
ntpr steps. The box dimensions (lengths and angles between the vectors)
is printed in the trajectory file. You can use "ncdump" to look at data
in NetCDF trajectories or just open an ASCII trajectory to look at the
box dimensions.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 10 2014 - 05:30:02 PDT
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