AW: periodic boundaries

From: Norman Geist (
Date: Tue Jul 10 2012 - 00:30:50 CDT



I think the usual way is to use the "Automatic PSF Builder" in VMD. You will
only need a pdb of your system and the parameter file/s.


For the PBC settings you have to know some kind of lattice constant for your
system to determine how to set the box dimensions that this lattice constant
will fit with the periodic copies.


Norman Geist.


Von: [] Im Auftrag
von farzad kiani
Gesendet: Samstag, 7. Juli 2012 12:51
Betreff: namd-l: periodic boundaries


Hi everybody

I've created a silicon box, using vmd software. How can I create psf file
from box in vmd main> extensions> modeling> inorganic builder, so this psf
file will run properly in namd2 How should I set periodic boundaries that
my silicon box extand Exactly.


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