VMD-L Mailing List

From: kirtana S (skirtana4_at_gmail.com)
Date: Fri Nov 11 2011 - 09:51:48 CST

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 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.
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 .

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.
>>
>
>