VMD-L Mailing List

From: kirtana S (skirtana4_at_gmail.com)
Date: Thu Nov 10 2011 - 23:49:47 CST

I am using your tutorials on
http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1
to construct the input files for LAMMPS .
I used scripts with slight modification to construct the input files for my
polymer chain.I used the output pdb file to check my bonds .

In the examples files for lammps in peptide , they have the bond and angle
coefficients specified separately in the data file whereas in your example
file the pair coeffients for methane monomers were were used in the input
file , do they detect that 1 is for CT and 2 for HC according to the
atomtypes from the data file.

Thanks
Kirtana
On Wed, Oct 12, 2011 at 5:46 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Oct 12, 2011 at 4:45 PM, kirtana S <skirtana4_at_gmail.com> wrote:
> > I am trying to build a lammps input file using the topotools tutorials .
> In
> > tutorial part 2 , how should I modify the .tcl
> > script to construct a chain instead of monomers.
>
> part 1 gives you an example for how to construct a bond list.
>
> http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-1#TOC-Step-1d:-Automatic-bond-detection-d
> if your chain is more complicated, you have to write additional Tcl code.
> the tutorial is by definition only showing you the principles;
> how you apply it to a real world case, is your job.
>
> cheers,
> axel.
>
> >
> > Thanks
> > kirtana
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>