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Bug #225

trjconv -ur compact doesn't work in gmx 4.0

Added by Anonymous about 12 years ago. Updated about 12 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Starting with gmx 332, trjconv -ur compact does not work with a dodecahedral box:

echo "CRYST1 50.000 50.000 50.000 60.00 60.00 90.00 P 1 1" > box.pdb
genbox -cp box.pdb -o w.pdb -cs spc216

  1. Does not work (same with gmx 3.3.3):
    echo 0|trjconv-4.0 -f w.pdb -s w.pdb -o c.pdb -ur compact
  1. works fine:
    echo 0|trjconv-331 -f w.pdb -s w.pdb -o c.pdb -ur compact

Cheers, Jochen

History

#1 Updated by Erik Lindahl about 12 years ago

You need to add the periodicity too (e.g. pbc atom, or -pbc mol if you also provide a topology) - then it works for me at least :) This was probably just version 3.3.1 silently assuming things...

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