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

[Erik Marklund]

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.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys