[gmx-users] how to visualize gromacs trajectory

[Stephani Macalino]

Hi,
Yes that command is right.
If you need to do other commands, the trjconv description and options are
in the second link I gave:
 http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-trjconv.html
Regards,
Stephani

On Tue, 9 Jul 2019 at 00:13, sunyeping <sunyeping at aliyun.com> wrote:

> 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:
>
>    1. First make your molecules whole if you want them whole.
>    2. Cluster your molecules/particles if you want them clustered.
>    3. 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
>    4. Center your system using some criterion. Doing so shifts the
>    system, so don't use trjconv -pbc nojump after this step.
>    5. Perhaps put everything in some box with the other trjconv -pbc or
>     -ur options.
>    6. 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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