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Bug #188

version 3.3.3: trjconv -pbc mol

Added by Rob Yang over 11 years ago. Updated about 11 years ago.

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

Created an attachment (id=275)
system in dodecahedron TIP5P water box

The system (in.gro) has a protein solvated in dodecahedron TIP5P water box. When using trjconv to visualize, the following options were tried and results shown:
trjconv -f in.gro -s in.gro -o out.pdb -pbc ? -ur compact
where ?
is:

-mol: intact protein, part of protein sticking out of the box, box is rectagular
-whole: intact protein, part of protein sticking out of the box, box is rectagular
-atom: intact protein, dodecahedron, protein completely inside the box (this is what I am expecting)

According to Dr. David van der Spoel, The -mol option should in theory produce the same output as the -atom option.

in.gro (8.65 MB) in.gro system in dodecahedron TIP5P water box Rob Yang, 03/07/2008 08:30 PM
bug188.tar.gz (9.1 MB) bug188.tar.gz input (including *.itp, *.top, *.gro, *.mdp, and *.tpr) Rob Yang, 03/10/2008 04:08 PM

History

#1 Updated by David van der Spoel over 11 years ago

I reproduced your findings.

Interestingly, the CVS branch of gromacs requires a tpr file for the mol option. Can you please upload a tpr file?

#2 Updated by Rob Yang over 11 years ago

Created an attachment (id=276)
input (including *.itp, *.top, *.gro, *.mdp, and *.tpr)

input files that includes the tpr file. I had deleted the in.gro file submitted initially from my files. So I re-prepared the same system with all the other input files including tpr. Thank you.

#3 Updated by Erik Lindahl about 11 years ago

Works in the 4.0 branch (tpr files are required, it might work in 3.3 too if you specify the -s option)

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