I have a data file for a lipid bilayer system in water (attached). It
runs fine as it is on the 10 April version of Lammps and the 28 Oct
version of Lammps.
I now want to replicate it in the x and y directions (ie to make a
bigger bilayer). The replicate command seems to do this in the 10
April version without error but if I try using replicate 2 2 1 in the
28 Oct version, I get the error "Bond/angle/dihedral extent > half of
periodic box length (domain.cpp:590)". I get this error whenever I
try and replicate in either the x or y directions; replicate in the z
direction works fine.
I don't understand why I'm getting this message as, according to my
reading of the manual, it means that the maximum extent of 2 bonds (I
have no dihedrals) is more than half the box side - but having
replicated, the box side is now twice the size it was when it worked.
I had a look back through this mailing list and it looks like a
similar question was asked on 18 September 2012 - but in that case the
error seemed to arise from restart files that might have been storing
the image flags in different ways depending on the version of Lammps.
I have no image flag data in data file I'm inputting. I've run the
system without any replication and dumped out the image flags for each
coarse-grained bead; all beads are initially in the 0,0,0 image.
Can anyone make any suggestions as to what might be going wrong and
how to fix it - there are features in the later version of Lammps I
need to use but I also need to reliably replicate the bilayer?
data.1024lip9216wat (3.32 MB)
forcefield.elba (2.25 KB)
in.elba (720 Bytes)