VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Wed May 05 2004 - 13:22:24 CDT

>>> "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.