[gmx-users] differences in plot between gromacs and vmd

[Shubhangi Gupta]

Hello,

        I have simulated a metalloenzyme, containing zinc, in gromacs for
100 ns. When i plot distance between zinc and a specific atom in protein,
the plots obtained are different in vmd and gromacs (using gmx distance).
vmd shows that the zinc has moved out of the protein at the end of
trajectory, whereas gromacs shows it is intact. How can the differences
between the two be accounted for?
 The plots are linked here.

https://www.dropbox.com/s/pwrpid0lwnewzet/vmd_image.png?dl=0
https://www.dropbox.com/s/1v2hzd1g62ldk4y/vmd_plot.png?dl=0
https://www.dropbox.com/s/b75xdgjlu2urb7y/xmgrace_plot.png?dl=0

Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

e-mail ID: ignahbuhs.gupta6 at gmail.com
               shubhangi_gupta at iitb.ac.in


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