VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 11 2011 - 10:14:23 CST

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.