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

2009-07-01 Thread 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 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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

2009-07-01 Thread Justin A. Lemkul 



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


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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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