[gmx-users] extra gro file generation

[Mirco Wahab]

On 05.11.2013 10:04, sarah k wrote:
> I'm going to perform a molecular dynamics simulation on a protein. As a
> default the simulation gives one final *.gro file. I need to get a .gro
> file after each say 500 ps of my simulation, in addition of the final file.
> How can I do so?
Riccardo already gave the important hints in another posting,
here are some additional explanations.

# first, generate an empty subdirectory in order to keep
# the simulation directory clean. The rm command is
# important if you repeat these steps

$> mkdir -p GRO/ ; rm -rf GRO/*.gro

# then, decide which part of the system you need:
# 0 - evgerything
# 1 - the protein
# 2 - the cofactor (if any)
# Remember: these numbers correspond to the order of molecules
# named in the .top-file. If your protein is "1" and you
# need only that, do a

echo "1" | trjconv -b 500 -noh -novel -skip 2 -sep -nzero 5 -o GRO/out.gro

# this will dump the system part "1" (the protein or whatever),
# starting from 500 ps (-b) and saving every 2'nd trajectory snapshot.

For each option to "trjconv" (-noh, -novel), please read the manual 
(where all of this can be found).

Regards

M.