Re: how to write the bond across the cell boundary

From: Ajasja Ljubetič (
Date: Fri Mar 25 2011 - 03:44:41 CDT

Dear all,

I too would like to know if this is possible (I'd like to make an endless
Any suggestion welcome.

Best regards,

2011/3/25 王棽 <>

> 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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