[gmx-users] the density of liquid benzene is too large

[Cenfeng Fu]

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
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