VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 18 2018 - 08:27:37 CDT

On Wed, Jul 18, 2018 at 8:47 AM Amir Hossein Saeedi Dehaghani <
mm229196_at_email.vccs.edu> wrote:

> ​Dear users and Axel
>
> I want to make a data file for lammps using *topo tool* package in vmd.
> My system consists of decan and benzene.
>
> However, when I make the data file an **additional** bond will appear.
>

​this means, that most likely you made a mistake at that step. please
explain in more detail how you "make" the data file, and best also provide
simple example file(s) to allow to reproduce the issue.​ decane and benzene
are simple enough molecules for that. depending on the force field you are
using, benzene may need special treatment anyway to ensure it maintains
sufficient planarity.

> I've already asked the lammps developers and they suggested deleting the
> individual bonds using **delbond** command.
> However, my system is *quite big *and so finding the wrong bonds and
> removing them individually would be so tedious!!
>

​this is why you have scripting in VMD. that can be used to automate tasks.
regardless, for simple molecules like decane and benzene, it is unexpected
that you have unwanted bonds unless you start from bad data or a bad
geometry.​

> Does anybody know how to delete a bond between a pair of *atom types*?
> Removing a specified bond type will be easy to perform.
>

​this can be easily done through processing the list of *all* bonds with
Tcl scripting. please note, that you would get better help, if you would
describe your problem better. from the description above it sounds like
there is a *single* additional bond, for which the topo delbond command is
the correct option. however, if you had said, that you want to remove a
whole list of bonds, that can be identified by the bond type, then topo
getbondlist followed by processing that list and then using topo
setbondlist would have been the recommended course of action, if there is
no way to provide correct input data (of which i am certain there is).

axel.

​

>
>
> Any hint is welcome.
> ​
>
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-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.