Creighton Buie wrote:
Hello Gromacs Community,
I am trying to set up a system where there is a coarse grained
hydrophobic polymer floor in a solvated water box. I am using the
martini force field with an .itp file for the polymer. The "floor" is
basically the polymer spaced 0.5 nm apart from each other and the bottom
bead is fixed in the X, Y, and Z direction. I have tried many ways of
fixing this bead using both freeze groups and position restrained
techniques, both to no avail. I am using PME and no part of the system
has a charge. The latest try has consisted of using the position
restrain line in the .itp file of the polymer through the topology file
and fixing the bottom bead with a force of 1000 in X Y Z. The energy
minimization run went smoothly but when I try to do any type of md I get
this error message:
"Not all bonded interactions have been properly assigned to the domain
decomposition cells
A list of missing interactions:
G96Angle of 432 missing 1
-------------------------------------------------------
Program mdrun, VERSION 4.0.3
Source code file: domdec_top.c, line: 172
Software inconsistency error:
Some interactions seem to be assigned multiple times
-------------------------------------------------------
"You Can Always Go On Ricky Lake" (Offspring)"
After searching the mailing list about this error I could only find that
it was a bug. Is this correct? Any suggestions is much appreciated.
If so, you should try an up-to-date version of GROMACS - 4.0.4 is current.
Mark
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