Dear All,
I want to simulate montmorillonite with lammps. First I created .car and .mdf file of the structure with Material Studio and then I used them to create data file with msi2lmp and clayff. But I get this warnings:
Forcefield file name: …/frc_files/clayff.frc
Output is recentered around geometrical center
Output contains style flag hints
System translated by: 0 0 0
Reading car file: mont.car
Reading mdf file: mont.mdf
Building internal coordinate lists
WARNING inconsistent # of connects on atom 16 type ob
WARNING inconsistent # of connects on atom 17 type ob
WARNING inconsistent # of connects on atom 22 type ob
WARNING inconsistent # of connects on atom 23 type ob
WARNING inconsistent # of connects on atom 28 type ob
WARNING inconsistent # of connects on atom 29 type ob
WARNING inconsistent # of connects on atom 34 type ob
WARNING inconsistent # of connects on atom 35 type ob
Reading forcefield file
Get force field parameters for this system
Unable to find equivalent type for ao
Unable to find equivalent type for ob
Unable to find bond data for ao ob
I searched this problem in mailing lammps, Jeff suggested delete bonds in the Material Studio before using msi2lmp. I have a question. If I delete bonds, would lammps detect which atoms should have nonbonded interactions? Because when I delete bonds, there is no bonds between atoms except O and H.
I definitely need help on this from lammps users.
Neda Sanchuli
Dear All,
I want to simulate montmorillonite with lammps. First I created .car and
.mdf file of the structure with Material Studio and then I used them to
create data file with msi2lmp and clayff. But I get this warnings:
Forcefield file name: ../frc_files/clayff.frc
Output is recentered around geometrical center
Output contains style flag hints
System translated by: 0 0 0
Reading car file: mont.car
Reading mdf file: mont.mdf
Building internal coordinate lists
WARNING inconsistent # of connects on atom 16 type ob
WARNING inconsistent # of connects on atom 17 type ob
WARNING inconsistent # of connects on atom 22 type ob
WARNING inconsistent # of connects on atom 23 type ob
WARNING inconsistent # of connects on atom 28 type ob
WARNING inconsistent # of connects on atom 29 type ob
WARNING inconsistent # of connects on atom 34 type ob
WARNING inconsistent # of connects on atom 35 type ob
Reading forcefield file
Get force field parameters for this system
Unable to find equivalent type for ao
Unable to find equivalent type for ob
Unable to find bond data for ao ob
I searched this problem in mailing lammps, Jeff suggested delete bonds in
the Material Studio before using msi2lmp. I have a question. If I delete
bonds, would lammps detect which atoms should have nonbonded interactions?
Because when I delete bonds, there is no bonds between atoms except O and
H.
you have to look up how interactions in clayff are modeled. the relevant
publication describing the force field has to tell you where explicit bonds
are needed and where not. from the looks of it (but don't take my word for
it), atoms of type ao and of type ob have no explicit bonds between them
and other atoms. so, your topology in the .mdf file doesn't seem consistent
with the force field and you get the errors as a consequence.
whether a pair of atoms interacts is independent of whether there is a
bond shown in the visualization.
axel.