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.gup...@gmail.com shubhangi_gu...@iitb.ac.in <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=default3&tag=caa22c94-ea74-4abf-a345-c66025e605d8> I’m protected online with Avast Free Antivirus. Get it here — it’s free forever. <https://www.avast.com/en-in/recommend?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail&utm_term=default3&tag=caa22c94-ea74-4abf-a345-c66025e605d8> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.