Calculating free energy of ion charging using compute fep

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1

All,

I’m trying to familiarize myself with the FEP capabilities of LAMMPS.

As a simple test case, I’m trying to calculate the free energy of charging of an isolated ion in a box of water. The starting point is a neutral LJ particle solvated in water. I want to run a simulation and calculate:

<U(q=1.0) - U(q=0.0)> in the uncharged state (And repeat the other way, and average).

Below is my input script for doing the calculation (the data file contains a 30x30x30 angstrom water box containing 890 water molecules and a single uncharged solute):

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Agilio will need to answer this (CCd). The naming conventions on the
compute fep doc page do not seem to match the names of

the pair styles in USER-FEP, e.g. there is no lj/soft or coul/soft.

I am guessing it is supposed to be lj/cut/soft and coul/cut/soft.

Steve

3

Hi Steve,

Thanks for your reply - I had a couple of updates:

I also tried to use coul/long/soft. That didn’t help. I still get (after minimization and equilibration run):
ERROR: compute fep pair style does not exist (…/compute_fep.cpp:215)

I then figured I need to declare this first in the pair_style - so, I modified the pair_style line as follows:

pair_style hybrid lj/cut/coul/long 10.0 10.0 coul/long/soft 1 10.0 10.0

Now, the simulation doesn’t start at all because it complains that: “ERROR: Pair hybrid sub-style is not used (…/pair_hybrid.cpp:421)” - I presume this is because the coul/long/soft substyle is not used initially. But, I need to use that only in the FEP calculation - so, I’m not sure how to do this calculation.

Thanks,
Sumanth

4

Hi Steve,

I’ve just answered to this post, explaining in detail how to use the core-softed pair styles.
Although there is no lj/soft or coul/soft in the documentation of the core-softer pair styles, I see that there is indeed mistake in the links from the compute_fep doc page. I’ll correct that right away.

Agilio