[gmx-users] trjconv and -pbc

[lina]

On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Lina,
>
> Make sure to use a reference in which the molecules are together (clustered)
> the way you want them.

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.lastname at gmail.com> wrote:
>
> Hi,
>
> I have a problem using
>
> trjconv_g -pbc nojump
> or
>
> trjconv_g -pbc nojump -center
>
> I even tried the -pbc whole.
>
> The system is protein with a small molecular, for the first time
> period, when I checked on pymol.
> they are together, but later they apart, after show cell, protein
> inside the cell, while this small molecular outside,
>
> I did not meet such issue before, it's used  to be easy to fix the pbc
> problem, but not this one. a bit surprise,
>
> They are supposed to be together,
>
> Thanks for any advice,
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>