Re: how to write the bond across the cell boundary

From: Axel Kohlmeyer (
Date: Fri Mar 25 2011 - 08:17:05 CDT

On Fri, Mar 25, 2011 at 4:44 AM, Ajasja Ljubetič
<> wrote:
> Dear all,
> I too would like to know if this is possible (I'd like to make an endless
> alpha-helix)
> Any suggestion welcome.

adding the bond should not be a problem with the .psf file.
i would not manually manipulate the .psf file with a text editor,
since that is rather error prone. you can define individual bonds
easily in VMD with: topo addbond <atom 1> <atom 2>
you have to be very careful with the simulation cell definition,
since that has now an impact on how much that bond is
stretched, and thus starting with a minimization is probably
a very good idea.

i don't know about NAMD, but i use LAMMPS a lot
these days and this method works perfectly there.


> Best regards,
> Ajasja
> 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

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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