[gmx-users] trjconv and -pbc

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Oct 28 06:34:28 CEST 2011

Hi Lina,

Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump

Hope it helps,


On Oct 28, 2011 6:27 AM, "lina" <lina.lastname at gmail.com> wrote:

On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsjerkw at 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).


> > Tsjerk > > On Oct 27, 2011 11:47 AM, "lina" <lina.lastname at gmail.com>
wrote: > > Hi, > > I have ...
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