Free energy of insertion

Hello lammps users,

I am trying to measure the free energy of insertion of a water molecules inside my system (difference in potential energy). I am using LAMMPS 21 Jan 2015 version. I am trying to achieve this in the following way

group network type 1:20:1

neigh_modify delay 0 every 1 check yes page 100000 one 2000 exclude group network network

fix 4 all deposit 100 0 1 342345 region 1 mol water attempt 1

This works fine.

Is there any other way ?

For example can the same be achieved using “include command” in neigh modify.

The manual is slightly unclear for me about the neigh modify include command. If we use the include command in the following way

group water type 21 22

neigh_modify delay 0 every 1 check yes page 100000 one 2000 include water

Does this build the neighbour lists for all the atoms in the water molecule or does it include only pairwise interactions within the group.
These are different.
Can someone please clarify ?

Thanks
Arun

Hello lammps users,

I am trying to measure the free energy of insertion of a water molecules
inside my system (difference in potential energy). I am using LAMMPS 21 Jan
2015 version. I am trying to achieve this in the following way

group network type 1:20:1
neigh_modify delay 0 every 1 check yes page 100000 one 2000 exclude
group network network
fix 4 all deposit 100 0 1 342345 region 1 mol water attempt 1

This works fine.

i don't think that what you get here is a free energy.

Is there any other way ?

have you looked at FEP? that i what i would expect people to use for
computing a free energy of insertion.

For example can the same be achieved using "include command" in neigh
modify.

The manual is slightly unclear for me about the neigh modify include
command. If we use the include command in the following way

group water type 21 22
neigh_modify delay 0 every 1 check yes page 100000 one 2000 include water

Does this build the neighbour lists for all the atoms in the water molecule
or does it include only pairwise interactions within the group.
These are different.
Can someone please clarify ?

the manual says: The include option limits the building of pairwise
neighbor lists to atoms in the specified group.
so all pairs between all atoms in the group water are considered. it
know nothing about a molecule named water. the default for building
neighbor lists is "include all", i.e. consider all atoms. of course
the usual exclusions and other modifications apply.

but i fail to see what this has to do with free energy calculations of
inserting water molecules.