Re: Periodic BCs

From: Alexander A. Vakhrushev (makaveli.lcf_at_gmail.com)
Date: Wed Sep 24 2008 - 12:58:40 CDT

Hi Navdeep!

 In my CNT flow simulations I simply use fixed atoms at both ends of
 CNT. The gap between atoms at the edge of periodic cell is set to
 length of CA bonds inside hexagonal carbon rings. Thus boundary atoms
 could not overlap. Perhaps it would help in your simulations.

 2008/9/24, Nd S <navdeep79_at_gmail.com>:

> 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
> other.
>
> Thanks
> Navdeep
>
> On Tue, Sep 23, 2008 at 6:11 PM, Jerome Henin <jhenin_at_cmm.chem.upenn.edu>
> 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
> > www.edam.uhp-nancy.fr/Alchemify), 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 <navdeep79_at_gmail.com> 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
> > >
> > >
> >
>
>
>
> --
> --------------------------------------------
> Gig'em
> Navdeep Singh
>

--
 Best regards,
 Dr. Alexander Vakhrushev
 Institute of Applied Mechanics
 Dep. of Mech. and Phys.-Chem.
 of heterogeneous media
 UB of Russian Academy of Sciences
 34 T. Baramzinoy St.
 Izhevsk, Russia 426067
 ----------------------------------
 С уважением,
    Вахрушев Александр Александрович
 к.ф.-м.н., с.н.с.
 Институт прикладной механики
 Уральского Отделения
 Российской Академии Наук
 426067, г. Ижевск
 ул. Т. Барамзиной 34
 +7(3412)21-45-83
-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous media
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067
----------------------------------
С уважением,
    Вахрушев Александр Александрович
к.ф.-м.н., с.н.с.
Институт прикладной механики
Уральского Отделения
Российской Академии Наук
426067, г. Ижевск
ул. Т. Барамзиной 34
+7(3412)21-45-83

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:48:20 CST