VMD-L Mailing List

From: ºÎع»Ô (he.yuhui.ime_at_gmail.com)
Date: Wed Dec 15 2010 - 03:37:53 CST

Dear All,

     I construct the pdb and psf files of a single-layer graphene, by
following the approach shown in the tutorial "Modeling Nanopores for
Sequencing DNA".

     (Maybe it is helpful to give more details for the construction: first,
the pdb file of a single-layer graphene is constructed by recording
positions of each carbon atom on the graphene; then, sigma-bonds are
determined and recorded by measuring the distance between each two carbon
atoms; after that, angles formed by two neighbouring sigma-bonds are
determined and recorded.
   I am aware that pi-bonds are not kept recorded of, since I have no idea
how to do that.)

   After the construction of graphene, I hope to merge it with some other
membrane such as SiN. Codes are as follows:

package require psfgen
resetpsf
readpsf $graphenePSF
coordpdb $graphenePDB
readpsf $sinPSF
coordpdb $sinPDB

# Write the combination.
writepdb $finalPdb
writepsf $finalPsf

    However, what I find in the final pdb is that nearly half of the
graphene carbon atoms have been moved to the coordinate origin, i.e, (0 0
0).

    Can anyone tell me what happens?

    Thanks very much! 

-- 
Ph. D He Yuhui  (ºÎع»Ô)
Institute of Scientific and Industrial Research, Osaka University;
Mihogaoka 8-1, Ibaraki, Osaka 567-0047. JAPAN