Re: waterbox

From: Marc Q. Ma (
Date: Wed Feb 22 2006 - 13:09:45 CST

i remember that i had suggested to you to visualize your system in your
original periodic cell. did you do that? waters travel to their
neighboring cells, and enter the original cell on the opposite side,
standard concept of PBC. please let us know your finding.

On Feb 22, 2006, at 11:57 AM, snoze pa wrote:

> Dear NAMD Users,
>  Anybody has any indea why my water box size is increasing in one
> direction and decreasing in other direction when I am doing free MD
> run.
> Here are the fig after minimization run. Though the water box is not
> getting distorted but its size is increasing in one direction, while
> in other it is shrinking
> at the same rate. I wondering why the water molecules from one
> oppoiste faces are moving towards the other opposite faces. Here are
> the link for snapshots
> namdmin.png
> and figure after 1ns run
> namd1ns.png
> I try to repeat simulation using useflexiblecell no, still problem
> remains same. My water box size is 10A in each direction from the edge
> of the molecule.
> Do I need to further increase the water boz size.
> thanks in advance

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