Transition mode visualizatiion

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helloworld
Transition mode visualizatiion

Hi,

In the documentation I found these commands for transition mode visualization but the tsmode_dimer.xyz file that I get is just a cluster of points. How can I visualise it better ?
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The transition mode can be visualised by writing a sequence in xyz format:
tsmode_xyz coords=ts_dimer.c coords2=tsmode_dimer.c \
n=20 delta=1. file=tsmode_dimer.xyz
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Also what is n and delta here ?
Any help would be appreciated.

Thank you,
Shreya

tomkeal
tomkeal's picture
Transition mode visualizatiion

Hi Shreya,

This command generates a sequence of XYZ structures which can be read in by a visualiser to view the transition state mode. For example in VMD you should be able to read in the file directly and then use the slider to move between frames to animate the mode.

In this command n is the number of frames in the sequence, and delta is the displacement along the mode. You can leave them at the defaults usually.

Best wishes,

Tom

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