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<stephanimacal...@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 <yepingsu...@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>> *
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