[gmx-users] NPT system density

[Moeed]

Hello,

I have 125 hexane molecules in a box of 0.25nm3. The desnity I calculate
from this number of molecules is approx. 71000 Kg/m3. To make sure that the
density remains constant I am doing NPT simulation. From this simulation I
see the density is 577 Kg/m3. and the volume is 30 nm3. Please guide me why
is this...also how can I get the compressibility for my system?


 *Volume                      30.9568   0.374111   0.204815  -0.108427
-1.08449
Density (SI)                577.914    6.97804    3.80252    2.02643
20.2684*


Thanks,



Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 21 data sets
The term 'Cons. rmsd ()' is averaged over 501 frames
All other averages are exact over 5001 steps

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle                       4390.56    265.163    204.663    58.3917
584.034
Ryckaert-Bell.              986.833    112.503    83.3767    26.1601
261.653
LJ-14                       649.581    30.9116    28.8685    3.82766
38.2843
Coulomb-14                 -289.755     25.871    9.19928     8.3746
83.7628
LJ (SR)                    -3367.85    62.5126    55.3718   -10.0486
-100.506
Coulomb (SR)                675.839    21.1543    7.92426   -6.79315
-67.9451
Coul. recip.                 927.32    22.6843    7.25885    -7.4434
-74.4489
Potential                   3972.53    379.824    316.992     72.469
724.835
Kinetic En.                 6331.94    257.353     242.79    29.5579
295.639
Total Energy                10304.5    567.222    484.728    102.027
1020.47
Temperature                 297.366     12.086    11.4021    1.38812
13.884
Pressure (bar)             -30.0299    746.524    745.665   -12.3992
-124.017
Cons. rmsd ()            3.73576e-06 2.80181e-07 2.35022e-07 5.28277e-08
5.28383e-07
Box-X                       4.98423  0.0200728  0.0109722 -0.00582152
-0.0582268
Box-Y                       2.49212  0.0100364  0.0054861 -0.00291076
-0.0291134
*Volume                      30.9568   0.374111   0.204815  -0.108427
-1.08449
Density (SI)                577.914    6.97804    3.80252    2.02643
20.2684*
pV                         -55.9879    1393.39    1391.81   -22.9985
-230.031
#Surf*SurfTen                218.21    4871.45    4871.37   -9.30662
-93.0848
T-HEX                       297.366     12.086    11.4021    1.38812
13.884
Lamb-HEX                    1.00011 0.000588089 0.000561362 -6.07045e-05
-0.000607166
Heat Capacity Cv:      12.5027 J/mol K (factor = 0.0016519)
Isothermal Compressibility: 0.00011012 /bar
Adiabatic bulk modulus:        9080.99  bar

mdp file:

title               = Hexane
cpp                 = /lib/cpp

;        Run control
integrator          =  md
dt                  =  0.002        ; ps !
nsteps              =  5000        ; total 1.0 ps.
nstcomm             =  1        ; frequency for center of mass motion
removal

;        Output control
nstenergy           =  10        ; frequency to write energies to energy
file. i.e., energies and other statistical data are stored every 10 steps
nstxout             =  10        ; frequency to write
coordinates/velocity/force to output trajectory file
nstvout             =  0
nstfout             =  10
nstlog              =  10        ; frequency to write energies to log file
nstxtcout          =  10

;        Neighbor searching
nstlist             =  10        ; neighborlist will be updated at least
every 10 steps
;ns_type             =  grid

;        Electrostatics/VdW
coulombtype         =  PME
vdw-type            =  cut-off
;        Cut-offs
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0

;        Temperature coupling    Berendsen temperature coupling is on in two
groups
Tcoupl              =  berendsen
tc-grps             =  HEX      ;sol
tau_t               =  0.1      ;0.1
ref_t               =  300      ;300

;        Pressure coupling:     Pressure coupling is not on
Pcoupl              =  berendsen
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0

;        Velocity generation    Generate velocites is on at 300 K. Manual
p155
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

;        Bonds
constraints         =  all-bonds
constraint-algorithm = lincs

pbc=xyz
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