Re: [AMBER] box information in .inpcrd and .rst files

From: David A Case <>
Date: Thu, 27 Oct 2011 08:10:02 -0400

On Wed, Oct 26, 2011, Giovanni Pavan wrote:
> When I visualize my periodic box and I measure from
> graphical interface the box dimensions, they are about 10% smaller than
> those listed at the bottom of the .inpcrd file. Why this?

If you are looking at an inpcrd file created by LEaP (say using the solvateBox
option), there is a deliberate gap between periodic boxes, in order to remove
bad overlaps. So, visualization might lead you to think that the box size is
smaller than it really is.

This effect should go away after presssure equilibration.

If you are looking at an equilibrated inpcrd file, then there is probably some
other explanation.


AMBER mailing list
Received on Thu Oct 27 2011 - 05:30:04 PDT
Custom Search