[gmx-users] SPC density

Mark Abraham mark.abraham at anu.edu.au
Thu Dec 29 01:47:06 CET 2011 

 
 
On 28/12/11, Theodora García <theodoraaagarcia at gmail.com> wrote:

> 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?

 
Indeed. You should find the paper in which the parameterization of SPC was reported, and seek to reproduce the density reported there with a similar model physics. In general, a water model was probably parameterized to reproduce a set of observables reasonably well, and it does none of them perfectly. In practice, around 0.98 is normal enough in my recollection.
 
Mark 
 

> 
> 
> 
> 
> 
> 
> 
> 
> 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(tel:%2B46184714205).
> > > spoel at xray.bmc.uu.se    http://folding.bmc.uu.se(http://folding.bmc.uu.se/)
> > > -- 
> > > gmx-users mailing list    gmx-users at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > 
> > 
> > 
> > 
> > 
> > 
> 
> 
> 
> 

 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111229/919860c2/attachment.html>

More information about the gromacs.org_gmx-users mailing list