Molecule topology type exceeds system topology type

Please keep the list in the loop.

yes, there have been dozens of patches and upgrades
since then. See the development version.


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:

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

See the create_box doc page for more details.