Hi,
I am modelling a simple bulk water system in lammps. I have used the LJ and coulomb cutoff pair potential styles with the SPC/E model of water and the respective parameters that i got from the documentation. I, however, also need to establish hydrogen bonds between the molecules and find out their number and their energies in the system.
Can somebody please suggest some method to do that in lammps, or otherwise ?
thanks,
prateek
If you mean adding in a hydrogen bond potential, then you probably shouldn’t, because then you’re breaking the SPC/E model. If you mean determining how many hydrogen bonds there are, and what their energies are, then post-processing using dump files is probably your best option. Presumably you have the formulas for the hydrogen-bond potential you want to use, and the definition of what constitutes a HB for that potential. Then it’s just a matter of programming it.
VMD might be able to do some of this for you, if the problem is correctly set up. I’ve found the interface balky to use, and I don’t know if it can calculate the energies according to an arbitrary formula.
–AEI
Hi,
I am modelling a simple bulk water system in lammps. I have used the LJ
and coulomb cutoff pair potential styles with the SPC/E model of water and
the respective parameters that i got from the documentation. I, however,
also need to establish hydrogen bonds between the molecules and find out
their number and their energies in the system.
well, first off,.hydrogen bonds are a "side effect" of the
lennard-jones potential
and charge distribution of the SPC/E model (as they are of a quantum chemistry
calculation); they are more a "concept" to describe an observable phenomenon,
i.e. that certain atom pairs are a bit more "sticky" and can form a network.
that being said, there is a _ton_ of literature on analyzing hydrogen bonds in
water and a lot of different variants of how to define and count them. as ahmed
said, this is best done in post-processing. there are a number of
tools available
that can do h-bond analysis, e.g. in VMD or with Gromacs. the energy
contributions you'll have to manually compute, but given the simple nature
of the SPC/E potential, this should not be trivial to do in a script or small
postprocessing program.
Can somebody please suggest some method to do that in lammps, or
otherwise ?
as being said before. hydrogen bonding in water is an intensely discussed
topic since the beginning of classical MD simulations of water in the 1970s,
so there is a wealth of material available. reading through a few reviews
should be a time well spent and help you avoid the many pitfalls. since
this is a well studied topic, you have to expect that any study of hydrogen
bonding will be placed under close scrutiny.
cheers,
axel.