From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Feb 22 2006 - 10:57:12 CST

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
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


and figure after 1ns run


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
Do I need to further increase the water boz size.
thanks in advance

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