From: Marzieh Alishahi (
Date: Sat Nov 17 2012 - 02:36:22 CST

Dear VMD-users

I've tried to create a silicon dioxide plate with VMD Inorganic builder
feature. Also I added bonds between Silicon and Oxygen with “Add bonds”
task. I tried to run this device with NAMD, but it seems the potentials
which are defined in SiO2.inp file are not sufficient to maintain the solid
molecules in their crystal structure. I saw the “Restraint Potential” which
is used in one of tutorials; “MODELING NANOPORES FOR SEQUENCING DNA”. I
added restraint potential to my configuration file. In this case, the
molecules remain in their positions but still no vibration for SiO2
molecules is shown.

I would be so grateful if anyone can help me how create this device in
order to have accurate vibration of SiO2 molecules. And if anyone can
recommend a reference about “Restraint Potential”! I’m really confused with
nature of this strong potential.

Any help is appreciated


Marzieh Alishahi