VMD-L Mailing List
From: Chenchen Wang (dvdcwangcc_at_gmail.com)
Date: Wed Apr 28 2010 - 15:15:38 CDT
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Hi,
I did what you told me to do, and it worked!
Thank you very much!
On Wed, Apr 28, 2010 at 11:37 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, 2010-04-28 at 10:39 -0400, Chenchen Wang wrote:
> > Hi,
>
> hi,
>
> please always keep the list in cc, so that people will see
> the resolution of a question.
>
> > I used the XYZ format as the input structure file which only has the
> > xyz coordinates of each atom in it.Then I loaded it,the correct
> > structure of polyethylene chain appeared on the display screen. I used
> > commands "topo numangles", it gave 0 as a result. So because I did not
> > provide angle/dihedral/improper information in my input file,then
>
> yes. where should it come from??
> already the bond information is not contained
> in your input and VMD is trying to guess it from
> a list of covalent radii under the assumption that
> you have covalent bonds and that the atom names that
> you are using are the names of the elements.
>
> > VMD would not give me these information?But I need these information
> > for the data. file in LAMMPS, can I get these information without
> > providing them? Is there a tool can do this?Because for a large
>
> for the most part, yes. there is a way to reconstruct this
> information, but you have to use and check this very carefully.
> in most force fields the definition of angle and dihedral
> potentials follows the bond topology and the atom types.
> if this is true in your case you can reconstruct those
> definitions using some of the topotools facilities.
> make sure that you have installed the latest version from:
> http://sites.google.com/site/akohlmey/software/topotools
>
> then you should first assign the atom types (you can do this
> by using appropriate atom names in your .xyz file) and
> then you should do "topo retypebonds" so that VMD can internally
> distinguish bonds between different atom types, that would
> otherwise get all the same (wrong) bond type. when VMD reconstructs
> bonds upon loading a file, it does not assign a bond type.
>
> next you can use "topo guessangles" and "topo guessdihedrals"
> to reconstruct the angle and dihedral definitions. apropriate
> types will be assigned automatically. there is also an
> option to guess impropers, but this is limited to a few cases.
> in general, those definitions require additional information
> from the force field data base.
>
> finally, you can use "topo writelammpsdata data.myfile full"
> or "topo writelammpsdata data.myfile molecular" to generate
> your lammps data file containing all the information that VMD
> has collected about your system in the process.
>
> i would _strongly_ suggest to try out this procedure with
> a very, very small system, where you can manually cross
> check that the multiple "guessing" steps are working correctly,
> before you try it on a real life problem. the package is fairly
> new and even though it has been working well and reliably
> for several people, there is always a chance of some
> "undocumented feature" when somebody uses them on a new problem.
>
> > system,it is really hard to count them by yourself...
>
> counting is only the minor issue. assigning the proper types
> consistently is much worse. this is why i wrote the plugin in
> the first place, since our group is working on surfactants
> where it is a similar necessity to generate the corresponding
> information.
>
> cheers,
> axel.
> >
> > Thank you!
> >
> > On Wed, Apr 28, 2010 at 5:46 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> > wrote:
> > On Wed, Apr 28, 2010 at 1:19 AM, Chenchen Wang
> > <dvdcwangcc_at_gmail.com> wrote:
> > > Hi,all
> > >
> > > I just started to use VMD, and I want to use the topotools
> > to get the
> > > topology information of polyethylene chain.But for number of
> > bonds,I get the
> > > correct information,but for angles,dihedrals and impropers,
> > it gives 0. I
> > > don't understand why.Can anyone help me with this?
> >
> >
> > VMD can only show you the information you provide
> > and this depends on the file format that you are using.
> >
> > please explain on more detail the steps that you perform
> > and the commands that you use and perhaps there is a
> > way to help you. with the present amount of information,
> > i can only say that you must be doing something wrong.
> >
> > cheers,
> > axel.
> >
> >
> >
> > > Angles:0 Dihedrals:0 Impropers:0 Cross-terms:0
> > > Bondtypes:0 Angletypes:0 Dihedraltypes:0 Impropertypes:0
> > >
> > > Thank you!
> > >
> >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> > http://sites.google.com/site/akohlmey/
> >
> > Institute for Computational Molecular Science
> > Temple University, Philadelphia PA, USA.
> >
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>
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