[gmx-users] the density of liquid benzene is too large
Cenfeng Fu
fucenfeng at gmail.com
Fri Oct 1 09:20:20 CEST 2010
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?
Thank you in advance!
Sincerely
Cenfeng Fu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101001/93b31552/attachment.html>
More information about the gromacs.org_gmx-users
mailing list