Hi,
I have been using VMD to generate my initial configuration data file for LAMMPS using topotools.
In the data file, I would also like to include the various pair_style, angle_style, etc. coefficients
for a particular force field (eg. OPLS-aa). For systems consisting of a few atom,angle,bond types its easy to do so manually,
but the task becomes very tedious for systems requiring larger number of parameters.
Is there any way of doing the above ?
Thanks,
Prateek Maheshwari
Third Year Undergraduate
Chemical Engineering Department
IIT Bombay
You could always write a script in Python or Perl (or other language of your choice) that reads in a data file that contains the force field info and parses your LAMMPS data file to figure out what kind of type info it needs. But without having the data already in a form where it can be processed, at least some manual entry will be required.
–AEI
You could also look at other tools in the lammps/tools directory
that automate this setup process. E.g. ch2lmp, msi2lmp, will generate
force field coeffs from CHARMM and MSI formats.
Steve
Hi,
I have been using VMD to generate my initial configuration data file for
LAMMPS using topotools.
In the data file, I would also like to include the various pair_style,
angle_style, etc. coefficients
for a particular force field (eg. OPLS-aa). For systems consisting of a few
atom,angle,bond types its easy to do so manually,
but the task becomes very tedious for systems requiring larger number of
parameters.
since you are already doing Tcl scripting, why don't you
just write a script from within VMD that will create the corresponding
pair_coeff, bond_coeff, angle_coeff lines and then use an "include"
statement. adding the coefficients to the data files is pretty clumsy
and in the case of pair_coeff has even serious shortcomings, since
you can only provide per-atom type parameters and not per pair.
with an include file you don't have to rely on mixing rules (which don't
apply to the force fields that i am working with).
cheers,
axel.