VMD-L Mailing List

From: kirtana S (skirtana4_at_gmail.com)
Date: Sat Nov 12 2011 - 02:01:26 CST

Yes I used VMD guessing algorithm through topotools scripts as in the
tutorials.
This works well with polymer chains by itself. Whereas when I use this for
polymer functionalized nanoparticle some undesired bonds were created . Can
you tell me how should I go about without using guess algorithm.

Thanks
Kirtana
On Fri, Nov 11, 2011 at 11:14 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Nov 11, 2011 at 10:51 AM, kirtana S <skirtana4_at_gmail.com> wrote:
> > Though pdb file contains no bond information , when I visualize the
> polymer
> > chain (pdb file) show the connectivity. If this is not the right way to
> test
>
> the connectivity that you see is "guessed" by VMD.
> most of the time VMD guesses correctly and in
> your case you may have used the VMD guessing
> algorithm through topotools in the first place to
> compute the bond topology. if you read in your
> data file using topo readlammpsdata then you
> get _exactly_ the bond topology. also if you save
> the topology information in a psf file, you can
> load this back and visualize it in combination
> with a pdb file (the most common way people
> use VMD).
>
> > this ,how should I go about.
> >
> > In the examples for peptide in lammps, the pair coefficients are
> specified
> > for 1 to 14 whereas they do not mention about the atom types.
>
> sure. the numbers are all the LAMMPS cares about.
> it is up to you to make sure they match. that is why
> people write a program to generate topologies for
> complex/large molecules. to do this manually would
> be far to error prone.
>
> > Whereas in your examples you have commented on the pair coefficients #1
> CT
> > . So when we write the bond coefficients how does the program recognize
> this
> > i.e 1 is for CT-HC bond .
>
> those comments are for _you_ to help
> with debugging. explanations are in the
> topotools documentation/tutorials and
> script code. if you don't understand it
> from that, you are out of luck, since
> i cannot explain it any other way.
>
> i repeat, all that lammps cares
> about are the numbers.
>
> cheers,
> axel.
>
> > Thanks
> > Kirtana
> >
> >
> > On Fri, Nov 11, 2011 at 8:27 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >>
> >>
> >>
> >> 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 .
> >>
> >> That is a pointless test. The pdb file contains no bond information.
> >>
> >>
> >> 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.
> >>
> >> I don't understand the question. When you set the coefficients for atom
> >> type 1 they will be used on atoms labeled as type 1 in the data file.
> The HC
> >> and CT strings are just comments.
> >> Axel
> >>
> >>
> >> 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.
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>