[gmx-users] how to visualize gromacs trajectory

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            Use “dynamic bonding” option from VMD, you can access it by vmd >> graphics >> representations >> drawing method >> choose DynamicBonds.Other way is make trajectory whole at every time stamp.RunGmx trjconv -f input.gro -o output.gro -s input.tpr -pbc mol Gmx trjconv -f input.xtc -o output.xtc -s input.tpr -pbc mol Then runVmd output.gro output.xtcDone-YogeshSent using Zoho Mail---- On Wed, 03 Jul 2019 09:53:05 +0530  Stephani Macalino<stephanimacalino at gmail.com> wrote ----Hello,It sounds like you have to fixed broken molecules and have problem withboundary conditions.After doing the MD, you need to fix your trajectory first before doingvisualization.Check this link for a workflow:http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_ConditionsAnd this:http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.htmlfor detailed trjconv command options.Regards,StephOn Wed, 3 Jul 2019 at 12:21, Sun Yeping <yepingsun80 at gmail.com> wrote:> Dear all,>> I wish to know what is the best way to visualize gromacs trajectory.>> When I load a gromacs trajectory into VMD, I find some of the water> molecules and some part of the protein in the system are streched and the> structure become weild and cannot be properly analyzed.>> I searched google and found there is a gromacs plugin for vmd, but I don't> know whether it will help improve gromcas trajectory visualization (>> https://www.ks.uiuc.edu/Research/vmd/plugins/updates/vmd192_gromacs_update1/> ).>> I also found there is a gromcas plugin for pymol (> https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/). But it seems> to be used for simulation. It doesn't seem to be used to load and visualize> a extraneous the gromacs trajectory.>> What are your suggestion？ Thank you in advance.>> Yeping> --> 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-request at 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 visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.