how to write the bond across the cell boundary

From: ═§Ś▓ (corarbor_at_163.com)
Date: Fri Mar 25 2011 - 01:52:15 CDT

Dear all:
I am writing the topology .psf file for an infinite large solid wall, I have to address the bond between the atoms at the boundary of the cell box so as to exclude the non-bonded interaction between these atoms. I have kept precise margin space for the box so as to keep the right distance for the atoms at the boundary. The serial indices for the bonded atoms, one of which is at the right end of the box and the other at the left end, were put in the !NBOND part of the .psf file. However, I got a "Bad global exclusion count errors" when I ran NAMD. I read the NAMD troubleshooting page about this error message. How can I, then, define the bonds between the atoms across the boundary at the psf file?
Cheers.
Wang Shen

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