Re: Periodic BCs

From: Nd S (
Date: Wed Sep 24 2008 - 12:01:48 CDT

Hi Jerome

I viewed the structure in vmd and found that the when viewed as a periodic
image the nanotube looks like a infinite long nanotube with bonds missing at
the ends of the box i.e. atoms at the end of one box are not bonded to the
atoms at the start of the second box, but atoms appear to be a bond distance
apart from each other.

Is there anyway in NAMD I can define that these atoms are bonded to each


On Tue, Sep 23, 2008 at 6:11 PM, Jerome Henin <>wrote:

> Hi Navdeep,
> If I were you, I'd do the following:
> 1) make sure that the PBC have atoms from the two ends exactly superimposed
> 2) apply strong harmonic positional restraints ("constraints" in namd
> lingo) to those overlapping atoms
> 3) tweak the PSF file (if you are using one) to define "nonbonded
> exclusions" between the overlapping ends, i.e. turn off their
> nonbonded interactions so that they won't clash.
> There is a relatively easy way to get point 3) done: make a PDB file
> of the full system, where you change the "B" value to 1.0 for C atoms
> at one end, and -1.0 at the other end. Then apply the program
> "alchemify" to your initial PSF file (see
>, using that PDB file as "fepFile".
> The program is initially designed for something else, but it should do
> the trick.
> Best,
> Jerome
> On Tue, Sep 23, 2008 at 6:38 PM, Navdeep <> wrote:
> > Hi
> >
> > I am working on carbon nanotubes, by putting it in a periodic box. The
> BC
> > are periodic. I am concerned that the nanotube is aligned in the z
> > direction, the atoms on the start of the nanotube and at the end of the
> > nanotube are different, but by the application of periodic BCs the atoms
> at
> > the end of nanotube in one box and the start of its periodic image
> virtually
> > share the same space. . How NAMD is going to handle this. Also there are
> no
> > bond defined between these atoms.
> >
> > Thanks
> > Navdeep
> >
> >

Navdeep Singh

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