Hi,
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).
Best,
Jochen
--
************************************************
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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