thank you for your detailed answer. Actually, it is a little difficult for
me to use moltemplate for my molecule( [BMIM][PF6] ionic liquid), since the
examples of moltemplate for Amber are not really helpful for my molecule(
with atm_style full). Could you please send me some example or tutorial
about amber for a bigger molecule.
This is a legitimate point. I made the AMBER force field available, but
I do not use it for my own work. So I do not have the time to make more
examples and test them, aside from the few that are already there.
I would love to solve this problem by crowdsourcing. I would love to
encourage people to submit their example molecules in moltemplate (or even
LAMMPS) format. If they do (either by email, or by github), I will include
them with moltemplate. If it would help to put a button on the moltemplate
web page along with a web form, I am happy to do that.
For now, if you do not mind switching force fields, then try the ATB
database. It contains molecule force field parameters and partial charges
for a huge variety of organic molecules in moltemplate (.LT) format. I
think it is free (for academic use). These molecules are presumably not
compatible with the AMBER force field.
BMIM is currently here:
(however they may change the URL in the future. If so, enter "BMIM" into
the search page)
Click on "Molecular Dynamics (MD) Files", and select "LAMMPS" from the
"Format" pull-down menu.