A rather simple but effective way is to make an index which contains 1/4
of your protein file. Use trjconv with -center tric -pbc whole/mol to
center that 1/4 of your protein and output the whole protein.
Tsjerk Wassenaar wrote:
Hi Bob,
You could try -pbc cluster. If that doesn't work, it'll be difficult.
The option -pbc nojump will only work on continuous trajectories.
Cheers,
Tsjerk
On 3/14/07, Robert Johnson <[EMAIL PROTECTED]> wrote:
Hello everyone,
I'm trying to visualze the conformations of a ssDNA molecule obtained
from a
REMD trajectory. As expected, there are parts of the simulation where
the
oligomer is broken due to the PBC wrapping. I've been trying to fix
this with
trjconv. However, the -pbc nojump option doesn't work - it actually
makes the
broken portions of the molecule worse and gives a terribly distorted
trajectory. Since the REMD trajectory isn't continuous (i.e. there are
instaneous jumps in the coordinates associated with REMD swaps), the
nojump
option may have problems. Does anyone know of any other way or other
tools that
I could use to reassemble my broken DNA strand?
Thanks,
Bob Johnson
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