[gmx-users] genbox and triclinic boxes. Problem an workaround.

Jochen Hub jhub at gwdg.de
Fri Aug 29 18:08:27 CEST 2008


there seems to be a problem when using genbox with triclinic boxes as 
solvent input. I have a frame 0.pdb from an equilibrated MD simulation 
of a triclinic box. When I take the water from the box as solvent input 
and the protein as "protein input" for genbox:

echo SOL | editconf -ndef -f 0.pdb -o sol.pdb
echo Protein | editconf -ndef -f 0.pdb -o prot.pdb

and then run:
genbox -cp prot.pdb -cs sol.pdb -o out.pdb

then an energy minization on out.pdb yields very large initial forces 
(like 1e+16). That should not be.

Making all molecules whole (via trjconv and a tpr) as suggested by the 
"known bug" of genbox does *not* help. What does help, however, is to 
run trjconv on the frame with -ur rect or -ur tric (not -ur compact).

Another weired issue is that genbox removes water molecules even if it 
reports that it removed zero water. By the way, the problem occurs in 
the 3.3.1 and in a quite recent CVS version (3.3.99_development_20080718).


Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

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