In order to chain the jobs, do i need to reference from the processed top
and last gro from the previous step. In other words, do i need to use :
pr2 step:
grompp \
-p ../pr1/molecule_pr1.top \
-c ../pr1/molecule_pr1.gro \
instead of (as above):
pr2 step:
grompp \
-p ../ini/molecule_ini.top \
-c ../ini/molecule_ini.gro \
I do use the new structure file in all of my chained jobs. The coordinates
in the structure file won't be being used because a .trr is supplied. For
an ensemble switch, the box size is not stored in the .trr IIRC, and the
only source of this information in the absence of an .edr file is the
structure file (hence the use of genbox). In your particular example, the
pre-NVT box will be the same size as the post-NVT box , so you shouldn't
have a problem here - but check it.
When you supply a trr file, the coordinates, velocities and box
will always be taken from the trr file.
The output from -pp should be functionally identical to its input, by
construction, so you can use any .top here. I omit the use of -pp and just
reuse the same .top all the time. This stops you hacking something once by
hand and forgetting to change other occurrences.
I presume i need to use the previous step top and gro parameters, but
using g_desort (not done yet).
Again in this case, is g_desort sufficient ?
Are -renum and -rmbdunbs only used for the run (but not permanently
affecting the top and gro files)?
Don't know.
grompp never modifies any of the input files.
Berk.
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