[gmx-users] umbrella sampling: pdo file not generated

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 1 20:29:02 CEST 2009

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.


> Thanks a lot,
> Gustavo
> ------ Dr. Gustavo Velardez Kemisk Institut Danmarks Tekniske Universitet
> (DTU) Danmark
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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