[gmx-users] trjconv - PBC

[Steven Neumann]

Thank you both!!!

Steven

On Mon, Oct 24, 2011 at 3:01 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Steven,
>
> Output can also be .pdb or .gro
>
> Cheers,
>
> Tsjerk
>
>  On Oct 24, 2011 3:59 PM, "Steven Neumann" <s.neumann08 at gmail.com> wrote:
>
> Sorry guys but I do not get this...
>
>
> I used:
>
> 1. First make your molecules whole if you want them whole
>
>
> trjconv -f md2.trr -s md2.tpr -pbc whole -o md2whole.xtc  (I have chosen
> my whole system for input and output)
>
>
>
> 2. I do not need cluster anything
>
> 3. Extract the first frame from the trajectory as reference for removing
> jumps if you want to remove jumps.
>
>
>
> trjconv -f md2whole.xtc -s md2.tpr -dump 0 -o md2wholeDUMP.xtc   ???
>
>
>
> I did not obtain any coordinate file as output can be only trajectory (trr
> or xtc file)
>
>
>
> 4. How to use this frame in:
>
>
>
> trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o
> md2wholeDUMPnojump.xtc ?????
>
>
>
> Please, help!
>
>
>
> Steven
>
>
>
>
>
>
> On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote: > > Hi, > > You don't n...
>
> --
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111024/3a4259b7/attachment.html>