Package to perform free energy calculations with LAMMPS. Includes core-softed versions of Lennard-Jones and Coulomb potentials, a technique to avoid singularities in many free-energy calculation routes. This has been integrated in the LAMMPS code.

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# compute fep for LAMMPS

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Package to perform free energy calculations with LAMMPS. Includes core-softed versions of Lennard-Jones and Coulomb potentials, a technique to avoid singularities in many free-energy calculation routes. This has been integrated in the LAMMPS code.

Dear Professor,

I am using your fdti.py tool to post process the result from the example CH4hyd, fdti01.

Below is your fdti.py file:

#!/usr/bin/env python

# fdti.py – integrate compute fep results using the trapezoidal rule

import sys, math

if len(sys.argv) < 3:

print ("Finite Difference Thermodynamic Integration (Mezei 1987)")

print ("Trapezoidal integration of compute_fep results at equally-spaced points")

print ("usage: fdti.py temperature hderiv < fep.lmp")

sys.exit()

rt = 0.008314 / 4.184 * float(sys.argv[1])

hderiv = float(sys.argv[2])

line = sys.stdin.readline()

while line.startswith("#"):

line = sys.stdin.readline()

v = 1.0

tok = line.split()

if len(tok) == 4:

v = float(tok[3])

lo = -rt * math.log(float(tok[2]) / v)

i = 0

sum = 0.0

for line in sys.stdin:

tok = line.split()

if len(tok) == 4:

v = float(tok[3])

hi = – rt * math.log(float(tok[2]) / v)

sum += (hi + lo) / (2 * hderiv)

lo = hi

i += 1

print (sum / i) # int_0^1: divide by i == multiply by delta

By comparing your script with the lammps compute FEP webpage, I could not figure out why you have hderiv here sum += (hi + lo) / (2 * hderiv) to calculate the area. Although I know hderiv is the charge perturbation value in the simulation.

Can you further elaborate ?

I would be really appreciated!

Best,

******************************************************************

Dezhao Huang

Ph.D. candidate at University of Notre Dame

MOlecular/Nano-Sacle Transport & Energy Research (MONSTER) Laboratory

Department of Aerospace and Mechanical Engineering

B14 Fitzpatrick Hall

Notre Dame, IN 46556-5710

Tel: (573)-578-0869

dhuang2@nd.edu