[gmx-users] How to calculate solvation energy?

[Saikat Banerjee]

Dear all,

I am trying to reproduce the ultrafast solvation dynamics of water.

I have run an 100ps NPT simulation of an equilibrated box of water
with 8 Na+ ions and 8 Cl- ions. The mdp file consists of two energy
groups - sodium(one Na+) and rest_system(all the remaining atoms). I
calculate the LJ-SR and Coul-SR between the two energy groups using
g_energy. Summation of the LJ-SR and Coul-SR and dividing by two gives
me the interaction energy. I calculate the correlation in the
fluctuation of that interaction energy. But, it does not capture the
ultrafast dynamics.

For my simulation, I have dt=0.002ps, nstenergy =2. I am running Gromacs 4.5.3

What am I doing wrong? Am I calculating the interaction energy
(solvation energy) properly? Is there any other way to get the
solvation energy?

For convenience, the mdp file is as follows:

; Run parameters
integrator      = md
nsteps          = 50000
dt              = 0.002

; Output control
nstxout         = 2
nstvout         = 2
nstxtcout       = 2
nstenergy       = 2
energygrps      = sodium rest_system
nstlog          = 2

; Neighborsearching
ns_type         = grid
nstlist         = 1
rlist           = 1.4
rcoulomb        = 1.4
rvdw            = 1.4

; Electrostatics
coulombtype     = PME
pme_order       = 4
fourierspacing  = 0.16

; Temperature coupling is on
tcoupl          = Nose-Hoover
tc-grps         = System
tau_t           = 0.2
ref_t           = 300

; Pressure coupling is on
pcoupl          = Parrinello-Rahman
pcoupltype      = isotropic
tau_p           = 2.0
ref_p           = 1.0
compressibility = 4.5e-5

; Periodic boundary conditions
pbc             = xyz

; Dispersion correction
DispCorr        = EnerPres

; Velocity generation
gen_vel         = no


Many thanks,
banskt

--
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Saikat Banerjee
Integrated Ph.D student
Prof B. Bagchi's group
Room no. 210
Solid State and Structural Chemistry Unit (SSCU)
Indian Institute of Science
Bangalore-560012

  Ph: +91-80-22933305 (lab)
      +91-80-23602338 (lab)
      +91-9980228606  (mobile)

  Alternate e-mail:
      saikat at sscu.iisc.ernet.in
      banskt at yahoo.co.in
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