[gmx-users] how to visualize gromacs trajectory

[sunyeping]

Hello, steph,

I have read the workflow for trajectory fixing at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, but I don't know how to perform these steps.
The workflow reads:

First make your molecules whole if you want them whole.
Cluster your molecules/particles if you want them clustered.
If you want jumps removed, extract the first frame from the trajectory to use as  reference, and then use trjconv -pbc nojump with that first frame as reference
Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step.
Perhaps put everything in some box with the other trjconv -pbc or -ur options.
Fit the resulting trajectory to some (other) reference structure (if desired), and don't use any PBC related option afterwards.
For the step 1, what this the command for keep the molecule whole? Should it be:
      gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_whole.xtc -pbc whole   ?
Could you give me some examples of the command for each step?

Thanks.

Yeping

------------------------------------------------------------------

From:孙业平 <sunyeping at aliyun.com>
Sent At:2019 Jul. 3 (Wed.) 17:39
To:gromacs <gmx-users at gromacs.org>
Subject:Re: [gmx-users] how to visualize gromacs trajectory

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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