Tutorial-l Mailing List

From: Hall McDull (jerviedog_at_gmail.com)
Date: Mon Apr 16 2012 - 00:03:05 CDT

Dear NAMD users,

I am learning how to set up the input files for the simulation on the
inorganic crystal surface. I came across the bionano tutorial which
introduces the method of setting up the input files for the silicon nitride
nanopore.

I have three questions about finding bongs in the silicon nitride crystal:

1. In the Appendix, there are some code as:
        # Find the internal bonds.
        puts "Bonding internal atoms..."
        set bond [bondAtoms all $bondDistance]
        puts "Internal bonds: [expr [llength $bond]/4]"
Here, why is the internal bonds equal to the total bonds divided by the
factor 4? why not 3.5? Because each silicon atom has 4 bonds, but each
nitrogen atom has 3 bonds.

2. Why there are no dihedral information in the PSF output? Won't this
cause problems in the simulation?

3. In the Appendix script, the atoms near the boundary are actually bonded
to atoms at the opposite boundary (please look at the drawing below, A is
bonded to B). Won't this cause problems in the simulation?

                              _____________
                             / \
                            / \
                           / A \
                          / \
                          \ B/
                            \ /
                              \ /
                                -----------------------

Thanks you all~

Jianfeng He

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