[gmx-users] SPC density

[Theodora García]

Dear all
I am starting some MD simulations aimed to calculate the volume of a solute
in water as a function of the concentration. First I ran a simulation of a
box with 4124 SPC water molecules (similar number of molecules that will be
later used with my solute) for which I got the following results after ~7.5
ns:

Statistics over 3762001 steps [ 0.0000 thru 7524.0005 ps ], 3 data sets
All averages are exact over 3762001 steps

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature                     298    125.156    125.156 1.9202e-05
0.144476
Volume                      126.908    53.2917    53.2917 5.61522e-06
0.0422489
Density (SI)                972.142    408.201    408.201 -4.30887e-05
-0.324199
Heat Capacity Cv:      16.9588 J/mol K (factor = 0.176389)
Isothermal Compressibility:   0.543909 /bar
Adiabatic bulk modulus:        1.83854  bar

Why am I obtaining so low density? The density seems to be constant over
that timescale.

This is my mdp file:

constraints         =  all-bonds
integrator          =  md
dt                  =  0.002
nsteps              =  2500000

nstxout             =  5000
nstvout             =  50000
nstenergy           =  1000
nstxtcout           =  5000
energygrps          =  SOL
nstlist             =  5

ns_type             =  grid
rlist               =  1.2
rcoulomb            =  1.2
rvdw                =  1.2
coulombtype         =  PME
fourierspacing      =  0.15
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes

Tcoupl              =  nose-hoover
tau_t               =  0.1
tc-grps             =  SOL
ref_t               =  298

Pcoupl              =  Parrinello-Rahman
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
pcoupltype          =  isotropic

gen_vel             =  yes
gen_temp            =  298
gen_seed            =  -1


Thanks in advance for any help...
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