Viewing in VMD

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1

I am running a simulation where i add a new atom every pico second. I
start with 960 atoms and after 1 pico second i have 961 and so on.
When i dump the trajectories and try to view in vmd i run into
problems because vmd can handles fixed number of atoms.

I am dumping into a .lammpstrj file for post processing. Is there a
way to work around it by dumping in some other format or some other
technique?

2

I am running a simulation where i add a new atom every pico second. I
start with 960 atoms and after 1 pico second i have 961 and so on.
When i dump the trajectories and try to view in vmd i run into
problems because vmd can handles fixed number of atoms.

I am dumping into a .lammpstrj file for post processing. Is there a
way to work around it by dumping in some other format or some other
technique?

you can split your trajectory into individual files per frame and use
the multiple molecule animation plugin in VMD.
http://www.ks.uiuc.edu/Research/vmd/plugins/multimolanim/

or you have to implicitly turn it into a fixed number of atoms again.
i've written a tool that handle it for simple .xyz style trajectories.
the downside of this approach is that
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readvarxyz-file-name-

this feature should be included if you have a recent version of VMD (1.9).
in case of problems you can update to the latest version from my homepage.

cheers,
    axel.

3

HI,

When i run the topo script i get the error

vmd > topo readvarxyz check.xyz
-error Problem with atom selection: Cannot find molecule -1 in
atomselect's 'molId'

now that indicates there was some failure to read. I was wondering if
i need to modify the dump file somehow before i run this script.

Thanks

Savio

4

HI,

When i run the topo script i get the error

vmd > topo readvarxyz check.xyz
-error Problem with atom selection: Cannot find molecule -1 in
atomselect's 'molId'

have you upgraded to the current version 1.2 snapshot of topotools?
it fixes a number of bugs in the 1.1 release (people with problems
always show up right _after_ a release, not before... :-/ ).

axel.

5

Hi,

Its working fine now.

Thanks

Savio