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 ...
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