Justin A. Lemkul skrev:
Gustavo Velardez wrote:
Hi all,
I ran a calculation using GROMACS 4.0.3 and this command line:
mpirun -np 8 mdrun_mpi -v -s $mol.tpr -pi $inp.ppa -pd $inp.pdo -po
pullout.ppa -pn index5000.ndx -g $mol.log > & $mol.out
I think everything is OK (it's working on GROMACS 3.3), but the pdo
file has
NOT been generated. How can I generate it from tpr, trr ou xct output
files? Is there another option to get the pdo file?
The pull code has changed substantially between version 3.3.x and
4.0.x; upgrade
to 4.0.5 (to take advantage of several bug fixes), read the
documentation and
revision history, and try again.
-Justin
Indeed. Some of those flags have completely different meaning now, and
others don't exist anymore. That should be obvious from mdrun -h.
/Erik
Thanks a lot,
Gustavo
------ Dr. Gustavo Velardez Kemisk Institut Danmarks Tekniske
Universitet
(DTU) Danmark
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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