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Bug #558

grompp -po writes to the directory of -p, not the working directory

Added by Mark Abraham about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

On git release-4-5-patches HEAD

grompp -f ../equilV.mdp -p ../../../preparation/topol.top -c ../../equilV.gro -pp here

writes here.top in ../../../preparation. It should be written in the directory in which grompp is run. -pp with no filename writes processed.top also in ../../../preparation.

Relevant output chunk below:

:-)  grompp_master  (-:

Option Filename Type Description
------------------------------------------------------------
-f ../equilV.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c ../../equilV.gro Input Structure file: gro g96 pdb tpr etc.
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndx Input, Opt. Index file
-p ../../../preparation/topol.top Input Topology file
-pp here.top Output, Opt! Topology file
-o topol.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file

History

#1 Updated by Berk Hess about 9 years ago

This bug should have been assigned to David, but I fixed it anyhow.

Berk

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