[gmx-users] trjconv - PBC

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 24 16:01:05 CEST 2011

Hi Steven,

Output can also be .pdb or .gro



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!


On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> > Hi, > > You don't n...

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