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

[Dallas Warren]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
https://twitter.com/dr_dbw/status/1066843191159050240
https://twitter.com/dr_dbw/status/909559339366572032

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Mon, 28 Jan 2019 at 16:49, Shubhangi Gupta <ignahbuhs.gupta6 at gmail.com>
wrote:

> 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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