On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps,
Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 > > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" <lina.lastn...@gmail.com> wrote: > > On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > Hi Lina, > > Make su... > > I used the initial mdrun .tpr. After checking the generated pdb (total > 51 frames), the first 28/29 frames both are together, but later are > separated. (the intra_fit also not work as expected). > > So I think at beginning the reference initial ones are together. > > This .xtc were trjcat together, first 200ns and then extend to 500ns, > the .pdb generated used dt 10ns. >> >> Cheers, > Am I wrong in some places? Actually for other trajectories I had no > problem (use the same way of handling it). > > Thanks, > >> > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" <lina.lastn...@gmail.com> >> > wrote: > > Hi, > > I have ... > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
<<attachment: Screenshot-2.png>>
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
