Maybe
trjconv -ur compact
could help you...
Cheers, Jochen
Sebastian Kruggel wrote:
Dear gmx-er,
I have problems creating (or visualizing) a dodecahedron box. I found simular
problems in the mailing list, where running mdrun is supposed to help - but
this does't work in my case.
I generated my box with the following commands
pdb2gmx -f $PROT.pdb -o $PROT.gro -p $PROT.top -ff oplsaa -water spce
editconf -bt dodecahedron -f $PROT.gro -o $PROT.ec.pdb -d 0.9
genbox -cp $PROT.ec.pdb -cs -o $PROT.b4ion.gro -p $PROT.top
grompp -f $MDP/em.mdp -c $PROT.b4ion.gro -p $PROT.top -o $PROT.b4ion.tpr
genion -s $PROT.b4ion.tpr -o $PROT.b4em.gro -nname Cl -nn 1 -g genion.log
# and after editing $PROT.top
grompp -f $MDP/em.mdp -c $PROT.b4em.gro -p $PROT.top -o em.tpr
mdrun -v -s em.tpr -o em.trr -c $PROT.b4pr.gro -e em.edr -g em.log
if I look at the tpr/trr with ngmx or chimera, the box is cubic and a very big
part of the protein is out of the box - I found in the mailing lists that this
shouldn't be a problem because of the periodic boundary conditions (even if
the manula says: 'Both -box and -d will center the system in the box').
I had a look at the tpr-file to see if it's maybe just a problem of
visualisation. I used gmxdump to look at the topology and found:
gmxdump -s pr.tpr | grep box
Reading
file pr.tpr, VERSION 3.2.1 (single precision)
box (3x3):
box[ 0]=
{ 8.77170e+00, 0.00000e+00, 0.00000e+00}
box[ 1]=
{ 0.00000e+00, 8.77170e+00, 0.00000e+00}
box[ 2]=
{ 4.38585e+00, 4.38585e+00, 6.20253e+00}
boxv (3x3):
boxv[ 0]=
{ 0.00000e+00, 0.00000e+00, 0.00000e+00}
boxv[ 1]=
{ 0.00000e+00, 0.00000e+00, 0.00000e+00}
boxv[ 2]=
{ 0.00000e+00, 0.00000e+00, 0.00000e+00}
So the box really looks dodecahedron in the first part, but what about the 0 0
0 boxv ?!?
Maybe somebody can help me figuring out if my box is 'really' dodecahedron?
Thanks in advance!
Sebastian
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--
************************************************
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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