[gmx-users] trjconv - PBC

[Steven Neumann]

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 need a .tpr file for removing jumps; a pdb/gro file will do.
>
> Cheers,
>
> Tsjerk
>
> On Oct 24, 2011 2:51 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
>
> Steven Neumann wrote: > > Dear Gmx Users, >  I am trying to convert my
> trajectory using trjconv.  ...
> trjconv -dump 0
>
> > > 3. Remove jumps if you want to have them removed using the first frame
> > >   > trjconv -f traj...
> Recreate the .tpr file using the coordinate file produced in (2).
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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