Re: Periodic BCs

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Sep 24 2008 - 14:51:18 CDT

Hi Navdeep,

What you're describing is exactly what Jerome suggested. The
positional restraints will somehow act as "bonding" terms at the ends
of your nanotube. In this case, you need to play a little bit with
different values of kf and see which one can effectively mimic the
bonding at both ends without destabilizing the system.

Cheers,
Michel

On Wed, Sep 24, 2008 at 7:01 PM, Nd S <navdeep79_at_gmail.com> wrote:
> 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
>

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