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 <sunyep...@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 <sunyep...@aliyun.com> > Sent At:2019 Jul. 3 (Wed.) 17:39 > To:gromacs <gmx-us...@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 <stephanimacal...@gmail.com> > Sent At:2019 Jul. 3 (Wed.) 12:24 > To:gromacs <gmx-us...@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 <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 > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@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 visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@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 visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or send a mail to gmx-users-requ...@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 visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.