VMD-L Mailing List

From: Cosmin ROMAN (cosmin.roman_at_imag.fr)
Date: Wed May 05 2004 - 17:34:23 CDT

My mistake John, I just tryed to find "vmd_frame" in the pdf and it didn't
show up. Sorry!

:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:._.:*~*:
:
   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: "Cosmin ROMAN" <cosmin.roman_at_imag.fr>
Cc: <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de>; <vmd-l_at_ks.uiuc.edu>
Sent: Wednesday, May 05, 2004 11:58 PM
Subject: Re: vmd-l: variable atom number and dynamic bonds

>
> Cosmin,
> Actually, the "trace" feature is documented pretty well even
> in the latest User's Guide. Have you seen this page?:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html#7338
>
> That page lists all of the traceable VMD state that you can easily
> get at from your own scripts.
>
> There's also a corresponding page for Python scripting:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node148.html#10424
>
> Regarding your idea to trace the frame variable and draw atoms yourself
> in your script, its certainly possible, though I'm sure that the
performance
> would be quite slow compared to what you're currently used to with VMD.
>
> Enjoy,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, May 05, 2004 at 11:53:56PM +0200, Cosmin ROMAN wrote:
> > 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
>
> --
> 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