Cenfeng Fu wrote:
Hello all,
I am simulating liquid benzene. Initially, I generate a cubic box with
600 benzene molecules in it. The length of the box is 4.6 nm. Then I do
the energy minimization and a NPT simulation for 20 ns. The force field
I used for benzene is OPLSAA (JACS,1990,112,4768). And here is my .mdp
file for the NPT simulation.
title = benz
cpp = /usr/bin/cpp
define =
integrator = md
dt = 0.002 ; ps !
nsteps = 10000000
comm_mode = Linear
comm_grps = System
nstxout = 0
nstvout = 2500
nstlog = 500
nstenergy = 50
nstxtcout = 500
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
vdwtype = cut-off
rvdw = 1.0
DispCorr = EnerPres
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
tcoupl = nose-hoover
ref_t = 300
tau_t = 0.5
tc_grps = System
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 3.0
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = yes
gen_temp = 300
gen_seed = 175298
constraints = hbonds
constraint_algorithm = LINCS
;shake_tol = 0.0001
lincs_order = 4
lincs_iter = 1
To my surprise, the density of the system is too large to the
experimental value (0.874 g/cm^3). Here are some results from the
g_energy command.
Statistics over 7500001 steps [ 5000.0000 through 20000.0000 ps ], 8
data sets
All statistics are over 750001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Potential 13996.9 15 302.701 -83.3695
(kJ/mol)
Temperature 299.976 0.00021 3.38239 -0.000582958 (K)
Pressure 1.08499 0.0072 1812.66 -0.026224 (bar)
Box-X 4.33432 0.00086 0.0102765 -0.00488475 (nm)
Box-Y 4.33432 0.00086 0.0102765 -0.00488475 (nm)
Box-Z 4.33432 0.00086 0.0102765 -0.00488475 (nm)
Volume 81.4276 0.049 0.579125 -0.275291 (nm^3)
Density 955.828 0.57 6.80024 3.23201
(kg/m^3)
Why the density is so large ? Could anyone give me some suggestions?
Several possible reasons:
1. The force field parameters aren't perfect, so there is some inherent
disagreement between simulation and reality. What is the expected value for
this force field?
2. You're using the isothermal compressibility for water. If your system is
pure liquid benzene, I'd think you would want to use the compressibility for
benzene. I don't know how big the difference would be off-hand, but at least
you'd be convinced that your simulation was set up properly.
3. Although it won't matter a huge amount, to what temperature does the
experimental density correspond? Usually these parameters are given at 25C (298
K). The temperature you've used is 300 K. Again, a minor point, but one worth
doing correctly in a simulation even though the such a change would not account
for the magnitude of difference you're currently seeing.
-Justin
Thank you in advance!
Sincerely
Cenfeng Fu
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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