[gmx-users] rhombic dodecahedron and very high pressures
Brian Curtis Stephenson
bcstephe at MIT.EDU
Fri Jan 27 06:03:42 CET 2006
Dear Gromacs Users,
I recently created a micelle and placed it in a rhombic dodecahedron box.
Visualization with VMD showed clearly that the micelle was solvated and was
placed within a dodecahedron volume of water as expected. The initial density
is very close to what would be expected at equilibration, as has always been
the case in the past when I use genbox -cs. However, as soon as I begin
simulation the dodecahedron increases in size very rapidly with both berendsen
and Parrinello-Rahman pressure coupling (with both isotropic and anisotropic
options, and with pbc=xyz or pbc=full). g_energy on the output reveals a very
high internal pressure in the cell. What could be going on? I've read a paper
by a group in China stating that they used pressure coupling in GROMACS with a
rhombic dodecahedron, so this should be supported. There doesn't appear to be
anything on the forums related to this, so I thought I would throw it out to
all of you users. Any help would be much appreciated!
Btw, I tested this with Gromacs-3.2.1 and a CVS version of GROMACS I use
regularly and both versions give the same problem.
My command sequence was:
genbox -cp start_file.gro -cs -o solv.gro -d 1.0 -p test.top
editconf -f solv.gro -bt dodecahedron -o dodec.gro
Visualization was done with:
trjconv -f dodec.gro -s topol.tpr -o vis.gro -ur compact
and everything showed up as expected.
Here's what g_energy gave for the pressures:
Pressure XX - bar
Pressure YY - bar
Pressure ZZ - bar
0.0000 35691 40510 42191
0.3000 9310 9656 9636
0.6000 and it keeps decreasing with time as the box expands....
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