Please keep the list in the loop.
yes, there have been dozens of patches and upgrades
since then. See the development version.
Steve
Ok, so I downloaded the developers version but I still get the same error as before. Maybe you get a different one because I only copied part of the submission script. In The attachment you can find the whole files.
Thank you very much for your help!
in.equilibrate.txt (2.9 KB)
solvoChain_l20.txt (722 Bytes)
Dear Steve,
I think you didn't get my email some weeks ago, so here it comes again.
I downloaded the development version from june 14th and I still get the same error:
ERROR: Molecule topology type exceeds system topology type (../molecule.cpp:1011)
This is my full input file:
# VARIABLES
variable T equal 1.0
# Initialization
units lj
boundary p p p
molecule scAB solvoChain_l20.txt
atom_style template scAB
region myBox block 0 100 0 100 0 100
create_box 2 myBox #bond/types 2
create_atoms 0 random 216 98734 myBox mol scAB 4852
print "neighbor lists"
neighbor 0.7 bin
neigh_modify every 1 delay 0 check no
print "Set interactions"
velocity all create ${T} 9822 #4674 #7654
# pair potentials
pair_style morse 5.000000 #cut-off 10e-8
pair_coeff 1 1 0.71400 1.8000 1.0000 4.466
pair_coeff 1 2 0.01785 6.0000 1.7500 2.372
pair_coeff 2 2 0.01785 6.0000 2.5000 3.122
pair_modify shift yes
bond_style fene/expand
#CAUTION HERE bonds fene ignores morse interaction between connnected monomers
special_bonds lj 1.0 1.0 1.0 #gives exact energy with MC
##special_bonds fene
bond_coeff 1 120.0000 0.6375 0.0000 0.0000 3.1875
bond_coeff 2 60.0000 0.7125 0.0000 0.0000 3.5625
print "Set simulation details"
fix therm all nvt temp $T $T 0.09
fix_modify therm energy yes
The manual explains this. Here in Section_errors.html
{Molecule toplogy/atom exceeds system topology/atom}
The number of bonds, angles, etc per-atom in the molecule exceeds the
system setting. See the create_box command for how to specify these
values.
See the create_box doc page for more details.
Steve