From: Qiang Fu (qiangfu.music_at_gmail.com)
Date: Mon Feb 28 2011 - 03:41:34 CST

Dear Dr. Kohlmeyer,

Thank you very much for your reply. I am sorry that I forgot to copy to the
mailing list. It will not happen again.

I really appreciate your help. After reading your words, I realized what
should do, and now the problem is well solved.

Best Regards!
Sincerely,
Qiang Fu

2011/2/25 Axel Kohlmeyer <akohlmey_at_gmail.com>

> please always copy the mailing list. i don't answer if people on
> the list don't get to see how a problem is resolved.
>
> On Fri, Feb 25, 2011 at 11:54 AM, Qiang Fu <qiangfu.music_at_gmail.com>
> wrote:
> > Dear Axel,
> >
> > If I was right, the method you proposed is to input the POSCAR file
> twice,
>
> you don't have to load the file twice. just create a second representation.
> if you don't know how to do that, read the VMD user's guide and work your
> way through the tutorials. there is no point in using a software without
> knowing
> what it does.
>
> > one for the VDW representation and the other for the DynamicsBomds one. I
> > tried it just now, and found that the bonds between metal atoms cannot
> > appear. I think that it is because in the DynamicsBomds mode, there is no
> > display for the metal atoms (Pt here).
>
> VMD has _no_ knowledge of chemistry. nada, zip, zilch.
> the dynamic bonds representation has an adjustable cutoff
> parameter. you have to set it to a proper value.
>
> axel.
>
>
> >
> > Best Regards!
> > Sincerely,
> > Qiang
> >
> > 2011/2/25 Axel Kohlmeyer <akohlmey_at_gmail.com>
> >>
> >> On Fri, Feb 25, 2011 at 10:48 AM, Qiang Fu <qiangfu.music_at_gmail.com>
> >> wrote:
> >> > Dear VMD Users,
> >> >
> >> > I want to draw a figure to show a molecule adsorbed on a metal
> surface.
> >> > However, there is no bond connection between metal atoms even I used
> >> > the
> >> > CPK mode for display, which makes the current version of the figure
> >> > unacceptable.
> >>
> >> have you tried using a VDW representation (with reduced radius)
> >> in combination with a DynamicBonds representation?
> >>
> >> axel.
> >>
> >> >
> >> > From the discussions on the VMD Mailing list, I know that with the
> >> > command
> >> > "topo addbonds <ID1> <ID2>, one can add a bond between the two atoms
> >> > <ID1>
> >> > and <ID2>. However, there are as many as 64 atoms in our surface
> system,
> >> > which makes it too complicated to achieve in the same way. I know the
> Tk
> >> > Console script might be used to do so, but I have very very little
> >> > knowledge
> >> > about it.
> >> >
> >> > Could you please give me some help? I am very grateful if you could
> tell
> >> > me
> >> > some convenient way to add bonds among so many atoms within the metal
> >> > surface. Thank you very much!
> >> >
> >> > Best Regards!
> >> > Sincerely,
> >> > Qiang Fu
> >> >
> >> >
> >> >
> >> > --
> >> >
> >> > Dr. Qiang Fu
> >> > Major in computational chemistry
> >> > E-mail: qiangfu.music_at_gmail.com
> >> > Profile URL: http://www.researcherid.com/rid/A-2557-2011
> >> >
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> Institute for Computational Molecular Science
> >> Temple University, Philadelphia PA, USA.
> >
> >
> >
> > --
> > Dr. Qiang Fu
> > Major in computational chemistry
> > E-mail: qiangfu.music_at_gmail.com
> > Profile URL: http://www.researcherid.com/rid/A-2557-2011
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>

-- 
Qiang Fu
Dept. of Theoretical Chemistry
Royal Institute of Technology
Stockholm, Sweden