[gmx-users] Free Energy Calculation

[Rabindra Oliya]

Dear Sir
I have been calculating free energy of molecular solid based on recent work
by J.L. Aragones, E.G. Noya, C. Valeriani and C. Vega (J. Chem. Phys. 139,
034104 (2013))
I am calculating it for methanol.
My .mdp file for production run is as  follows
title                    = EM alpha methanol
integrator               = md
tinit                    = 0
dt                       = 0.001
nsteps                   = 5000000
init_step                = 0
comm-mode                = none
nstcomm                  = 1
comm-grps                =
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
nstlog                   = 10000
nstenergy                = 10000
nstxtcout                = 10000
xtc-precision            = 10000
nstlist                  = 1
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
domain-decomposition     = no
coulombtype              = pme
rcoulomb                 = 1.0
pme_order                = 4
fourierspacing           = 0.1
vdw-type                 = cut-off
rvdw-switch              = 1.0
rvdw                     = 1.0
DispCorr                 = EnerPres
Tcoupl                   = v-rescale
tau_t                    = 2
ref_t                    = 150
tc-grps                  = system
Pcoupl                   = no
gen_vel                  = yes
gen_temp                 = 150
gen_seed                 = 3414125
constraints              = all-angles
; Type of constraint algorithm
constraint-algorithm     = lincs
lincs-iter               =  4
lincs-order              =  6
freezegrps = SH3
freezedim  = y y y

After production run I need to extract energies from the GROMACS trajectory
file (as they suggested) .
How can this be done?

Rabindra Raj Oliya
Tribhuvan University
Nepal