[gmx-users] SPC density

[Theodora García]

Thank you very much for your advice... I have tried including dispcorr =
enerpres in my mdp file and the density increased a bit in a timescale of 5
ns but it is still far from the value expected for pure water. These are
the new results:

Statistics over 2500001 steps [ 0.0000 thru 5000.0000 ps ], 3 data sets
All averages are exact over 2500001 steps

Energy                      Average       RMSD     Fluct.      Drift
Tot-Drift
-------------------------------------------------------------------------------
Temperature                     298    2.67563    2.67534 2.70867e-05
0.135433
Volume                      126.133   0.529594   0.529323 1.17324e-05
0.0586622
Density (SI)                978.114    4.10621    4.10412 -9.08266e-05
-0.454133
Heat Capacity Cv:      12.4733 J/mol K (factor = 8.06157e-05)
Isothermal Compressibility: 5.40447e-05 /bar
Adiabatic bulk modulus:        18503.2  bar

I guess I should get 1000 g/cm^3

Any other suggestion?




On Tue, Dec 27, 2011 at 6:23 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> 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
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