[gmx-users] how to visualize gromacs trajectory

[sunyeping]

Hi, Steph

I used the following command to repair the trajectory:

gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center  -pbc mol -ur compact

the bond stretching has disappeared, but the subunits of the protein seperate from each other. How to deal with this? Would it be useful to repeat the trjconv command?

Yeping

------------------------------------------------------------------
From:Stephani Macalino <stephanimacalino at gmail.com>
Sent At:2019 Jul. 3 (Wed.) 12:24
To:gromacs <gmx-users at gromacs.org>
Subject:Re: [gmx-users] how to visualize gromacs trajectory

Hello,
It sounds like you have to fixed broken molecules and have problem with
boundary conditions.
After doing the MD, you need to fix your trajectory first before doing
visualization.
Check this link for a workflow:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions


And this:
http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
for detailed trjconv command options.
Regards,
Steph


On 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
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