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.war...@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.gup...@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.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. -- 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.
