[gmx-users] How to calculate solvation energy?
Saikat Banerjee
banskt.saikat at gmail.com
Tue Feb 1 08:20:16 CET 2011
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
--
-------------------------------------------------------------------
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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