-pbc atom Date: Fri, 28 Oct 2011 06:34:28 +0200 Subject: Re: [gmx-users] trjconv and -pbc From: tsje...@gmail.com To: gmx-users@gromacs.org
Hi Lina, Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump Hope it helps, 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
-- 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
