[gmx-users] SPC density

[Theodora García]

Hi
I just saw the article "Temperature Dependence of TIP3P, SPC, and TIP4P
Water from NPT Monte Carlo Simulations: Seeking Temperatures of Maximum
Density" published in Journal of Computational Chemistry, Vol. 19, No. 10,
1179]1186 (1998). It gives 0.985 for SPC at 25 C with different setup...
perhaps 0.978 is not so bad?





On Wed, Dec 28, 2011 at 9:34 AM, Theodora García <theodoraaagarcia at gmail.com
> wrote:

> 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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>
>
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