Annealing process of silica with excluded block

From: Marzieh Alishahi (
Date: Fri Sep 12 2014 - 10:22:51 CDT

Dear NAMD users,

 I want to perform “Annealing” process on a silica (Silicon Dioxide) solid
material which was primarily created by Inorganic Builder toolbox on VMD
and the point is that the silica is a cube with a smaller cube cut out from
the upper corner. That means at the upper surface of silica, there is a
part of excluded volume, so I cannot use “wrapAll on” in my NAMD
configuration file. And if I turn off the “wrapAll” command, the silica
molecules will pass the boundaries during annealing process. I Also try
adding restrain on silica atoms, but it seems somehow meaningless since it
will cancel all the movements of atoms during annealing. I would be so
grateful if any one could help me to solve this problem.

 Thanks in advance,


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