[gmx-users] SPC/E water RDF

Francisco Garcia garcia.ff.000 at gmail.com
Fri May 28 12:05:19 CEST 2010

Dear users,

Since I'm new to MD, I coded SPC/E water in the NVT emsemble.

Basic ingredients:

(1) Number of water molecules N=216
(2)   Mass of O = 16
      Mass of H = 1
(3)   Box density (Periodic Boundary Condition) is exactly 1g/cc (L
=18.6205 Angstrom)
(4)   SPC/E LJ parameters from Berendsen's original 1987 paper
(5)   Coulomb interaction: Ewald sum
      Real space ewald: Minimum image convention
      Ewald convergence parameter for reciprocal sum = 5/L (L is the
box length in Ang)
      Fourier cut-off for ewald reciprocal sum |G| =2*pi*|n|/L, where |n| < 27
(6)   Nose-Hoover chain NVT (single chain, single thermostat per chain)
(7) Time step 1 fs, velocity verlet solver, RATTLE was used to
constrain bond lengths and angle, and correct velocities.
(8) 100 ps equlibration, 400 ps production (configuration was saved every 25 fs)

Everything is fine (energies are stable, etc.) except the second peak
in the O-O rdf.
The first peak is fine but my second peak seems flat. I find this
troubling since
all the rdfs I've seen in literature as well the experimental plot
have a well-defined
second peak. I must mention that in all the papers I've seen the
ensemble is NPT (I've not seen NVT yet). In any case, I was expecting my result
to match previously published results closely.

Can anyone point out what I am doing wrong?? Is NVT not a good ensemble
for water simulation?? I'll appreciate it if someone can refer me to a paper
that discusses this.

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