VMD-L Mailing List

From: Cosmin ROMAN (cosmin.roman_at_imag.fr)
Date: Wed May 05 2004 - 16:53:56 CDT

Thank you Axel and John,

To Axel: You should have mentioned your own site and CPMD-VMD as well. I
think there are plenty of interesting things and non-typical VMD situations
addressed in your collection of scripts. About dummy atoms I can't tell that
it didn't cross my mind but it seemed rather painful since it involved
post-processing the trajectory file. Since the code generating the
trajectories is mine and since John's solution involves having the whole set
of atoms from the beginning as well, I will try to generate this file
accordingly.

To John: I will praise the creators of vmd once more for giving us a truly
wonderful tool, but wonder at the same time why do they keep hiding all its
powerful features away from us. The 1.3 documentation version was the last
one mentioning about vmd_frame and the tracing mechanism. I simply didn't
know that's possible!

I have a question for you both. How much ineffective would be to trace the
vmd_frame and draw for each frame the set of spheres representing my atoms
(eventually even the cylinders for bonds) considering a "very open" system,
i.e. a system intensively exchanging atoms with its environment?

Thank you again,

Regards,

Cosmin.

P.S. Axel, I was going to suggest you to use the User property of atomselect
(undocumented) which interestingly is a per frame property, to map the
charges on atoms avoiding thus using the vmd_frame tracing (Section 5.3).
John explained me once how to do this since it's not in the documentation,
so if you want I'll forward you his mail.

:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
:
   Cosmin ROMAN, Ph.D. Student.
:
   TIMA-INPG, MNS Group,
: 46 Avenue Félix Viallet,
   38031 Grenoble Cedex, FRANCE.
:
   Tel : 00 33 4 76 57 48 34
: Fax : 00 33 4 76 47 38 14
   e-mail : cosmin.roman_at_imag.fr
:
:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Axel Kohlmeyer" <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de>
Cc: <vmd-l_at_ks.uiuc.edu>; "Cosmin ROMAN" <cosmin.roman_at_imag.fr>
Sent: Wednesday, May 05, 2004 10:49 PM
Subject: Re: vmd-l: variable atom number and dynamic bonds

>
> In addition to Axel's suggestion, one might consider setting the "User"
field
> with a Tcl script, with a 1.0 or 0.0 to indicate if the atom "exists" and
> then use an atom selection with "user > 0.0" to only draw atoms that
exist.
> (don't forget to enable the "update selection every frame" button in the
> trajectory tab...)
> That might be preferable to using special atom coordinates, since they'll
> alter VMD's default viewing/scaling behavior, among other things.
> In the longer term, I'd like to come up with a better solution for this
> sort of thing, but there's no convenient way to retrofit VMD to handle
this
> that's non-intrusive, so tricks like using the atom coordinate or User
field
> with atom selections are probably the best short-term solution.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, May 05, 2004 at 08:22:24PM +0200, Axel Kohlmeyer wrote:
> >
> > >>> "CR" == Cosmin ROMAN <cosmin.roman_at_imag.fr> writes:
> >
> >
> > CR> Hello,
> >
> >
> >
> > CR> Is there any possibility (or trick) to dynamically create and
destroy =
> > CR> atoms during an animation in VMD? For instance when simulating open
=
> > CR> systems one would often find himself in such a situation, i.e.
having =
> > CR> atoms going in and out of the simulation box continuously. Also, the
=
> > CR> bonds in this case should be updated dynamically. Can one set the
number =
> > CR> of atoms and the bonds for each frame individually? (When I am
talking =
> > CR> about dynamic bonds I am not referring to the drawing method having
this =
> > CR> name but rather to a more controllable version in which the user
could =
> > CR> provide the full list of bonds per frame.)
> >
> >
> > CR> My input file is a generalized multi-frame XYZ file having different
=
> > CR> atom number and species for each frame.
> >
> >
> > hi,
> >
> > not directly. the best i can think of, is to rewrite the
> > trajectory file to contain a constant number of atoms, but
> > to put the additional dummy atoms far away, say at z=-200.0
> > and then use selections that have the additional requirement
> > 'and z > -199.0'. note that the 'identity' of the atom type
> > is only taken from the first frame, so that you have to add
> > enough dummy atoms for all atom types, that you need.
> >
> > as for the dynamic bonds visualization, if you use several
> > of these visualizations with different selections, you can
> > create quite controlled bonds.
> >
> > other than that, you'd have to set the bonds fresh
> > for each frame by tracing vmd_frame, which would be
> > quite a performance killer.
> >
> > hope this helps,
> > axel kohlmeyer.
> >
> >
> >
> > CR> Thank you for your support and patience,
> >
> > CR> Regards,
> >
> > CR> Cosmin
> >
> >
> >
> >
> > CR> :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> > CR> :=20
> > CR> Cosmin ROMAN, Ph.D. Student. =20
> > CR> :
> > CR> TIMA-INPG, MNS Group,
> > CR> : 46 Avenue F=E9lix Viallet,
> > CR> 38031 Grenoble Cedex, FRANCE.
> > CR> :
> > CR> Tel : 00 33 4 76 57 48 34
> > CR> : Fax : 00 33 4 76 47 38 14
> > CR> e-mail : cosmin.roman_at_imag.fr
> > CR> :
> > CR> :*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
> > CR> ------=_NextPart_000_0B5B_01C432CA.20F2C460
> > CR> Content-Type: text/html;
> > CR> charset="Windows-1252"
> > CR> Content-Transfer-Encoding: quoted-printable
> >
> > CR> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
> > CR> <HTML><HEAD>
> > CR> <META http-equiv=3DContent-Type content=3D"text/html; =
> > CR> charset=3Dwindows-1252">
> > CR> <META content=3D"MSHTML 6.00.2800.1106" name=3DGENERATOR>
> > CR> <STYLE></STYLE>
> > CR> </HEAD>
> > CR> <BODY bgColor=3D#ffffff>
> > CR> <DIV><FONT face=3DArial size=3D2>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Hello,</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN>&nbsp;</P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Is there any
possibility =
> > CR> (or trick)=20
> > CR> to dynamically create and destroy atoms during an animation in VMD?
For =
> > CR> instance=20
> > CR> when simulating open systems one would often find himself in such a
=
> > CR> situation,=20
> > CR> i.e. having atoms going in and out of the simulation box
continuously. =
> > CR> Also, the=20
> > CR> bonds in this case should be updated dynamically. Can one set the
number =
> > CR> of=20
> > CR> atoms and the bonds for each frame individually? (When I am talking
=
> > CR> about=20
> > CR> dynamic bonds I am not referring to the drawing method having this
name =
> > CR> but=20
> > CR> rather to a more controllable version in which the user could
provide =
> > CR> the full=20
> > CR> list of bonds per frame.)</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN>&nbsp;</P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">My input file is a =
> > CR> generalized=20
> > CR> multi-frame XYZ file having different atom number and species =
> > CR> for&nbsp;each=20
> > CR> frame.</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN>&nbsp;</P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thank you for your
support =
> > CR> and=20
> > CR> patience,</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Regards,</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: Arial">Cosmin</SPAN></P>
> > CR> <P class=3DMsoNormal style=3D"MARGIN: 0cm 0cm 0pt"><SPAN
lang=3DEN-US=20
> > CR> style=3D"FONT-SIZE: 10pt; FONT-FAMILY: =
> > CR> Arial"></SPAN></FONT>&nbsp;</P></DIV>
> > CR> <DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
> > CR> <DIV><FONT face=3DArial =
> > CR> size=3D2>:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:<BR>:=20
> > CR> <BR>&nbsp;&nbsp; Cosmin ROMAN, Ph.D.=20
> > CR> Student.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; =
> > CR> <BR>:<BR>&nbsp;&nbsp;=20
> > CR> TIMA-INPG, MNS Group,<BR>:&nbsp; 46 Avenue F=E9lix =
> > CR> Viallet,<BR>&nbsp;&nbsp; 38031=20
> > CR> Grenoble Cedex, FRANCE.<BR>:<BR>&nbsp;&nbsp; Tel : 00 33 4 76 57
48=20
> > CR> 34<BR>:&nbsp; Fax : 00 33 4 76 47 38 14<BR>&nbsp;&nbsp; e-mail :
<A=20
> > CR>
href=3D"mailto:cosmin.roman_at_imag.fr">cosmin.roman_at_imag.fr</A><BR>:<BR>:*~=
> > CR>
*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:</FONT></DIV></BODY></HTML>
> >
> > CR> ------=_NextPart_000_0B5B_01C432CA.20F2C460--
> >
> >
> >
> > --
> >
> > =======================================================================
> > Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> > D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078