[gmx-users] SPC density

[David van der Spoel]

On 2011-12-27 17:57, Theodora García wrote:
> 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:

dispcorr = enerpres
>
> 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...
>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se