[gmx-users] interaction energy of bulk TIP3P

[sandeep somani]

Hi All

I simulated a cubic box of 2180 TIP3P water molecules using gmx 3.3 and PME
for 400 ps and extracted the interaction energy of a randomly picked water
molecule with rest of the system.
Simulation was done at 298K and 1bar and usual procedure for generating a
water box and equilibration were used.

Average interaction energy reported in the log file was
Epot (kJ/mol)        Coul-SR          LJ-SR
      WAT-rest   -8.13828e+01    1.21886e+01

giving a total of          -8.13828e+01  + 1.21886e+01 = -69.194 kJ/mol

Comparing with published numbers using other MD programs this should be in
the range of -81 +/- 1 kJ/mol i.e. ~11 kJ/mol less.

any clues on origin of this discrepancy ?  relevant .top , .mdp files are
below.

Thanks
Sandeep


;-----------------------
*;MD.MDP for bulk TIP3P *
;-----------------------
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
tinit               =  0.0
dt                  =  0.002
nsteps              =  200000 ; 400  ps
nstcomm             =  1
nstxout             =  50
nstlog              =  50
nstenergy           =  50
nstxtcout           =  50
nstlist             =  5
energygrps          =  WAT
ns_type             =  grid
;PME
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
; Temperature coupling
Tcoupl              =  berendsen
tc-grps             =   SOL WAT
tau_t               =   0.1 0.1
ref_t               =  298  298
; Pressure coupling is on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
;-----------------------
*; TOP FILE FOR TIP3P BULK *
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include water topology
#include "tip3p.itp"
[ system ]
; Name
bulk water
[ molecules ]
; Compound        #mols
SOL                 2180
----------------------

*bits of log file from production run:*

       <======  ###############  ==>
       <====  A V E R A G E S  ====>
       <==  ###############  ======>

  Energies (kJ/mol)
       LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
   1.35174e+04   -8.91571e+04   -1.10392e+04   -8.66790e+04    1.61998e+04
  Total Energy    Temperature Pressure (bar)
  -7.04792e+04    2.97985e+02    2.27514e+00

         Box-X          Box-Y          Box-Z         Volume   Density (SI)
   4.06327e+00    4.06327e+00    4.06327e+00    6.70858e+01    9.72133e+02
            pV
   9.03527e+00

  Total Virial (kJ/mol)
   5.40366e+03   -6.97436e+00    2.78681e+00
  -6.97436e+00    5.38940e+03   -2.37439e+00
   2.78681e+00   -2.37439e+00    5.39318e+03

  Pressure (bar)
  -2.28378e+00    3.27978e+00   -1.13390e+00
   3.27978e+00    4.65423e+00    1.52221e+00
  -1.13390e+00    1.52221e+00    4.45496e+00

  Total Dipole (Debye)
   3.23351e+00   -1.12569e+01    1.42062e+01

 Epot (kJ/mol)        Coul-SR          LJ-SR
       WAT-WAT    0.00000e+00    0.00000e+00
      WAT-rest   -8.13828e+01    1.21886e+01
     rest-rest   -8.90758e+04    1.35052e+04

         T-SOL          T-WAT
   2.97985e+02    2.97422e+02


       M E G A - F L O P S   A C C O U N T I N G

  RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
  T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
  NF=No Forces

Computing:                        M-Number         M-Flops  % of Flops
-----------------------------------------------------------------------
Coul(T) + LJ [W3-W3]          21419.733112  8182338.048784    66.4
Outer nonbonded loop           3168.782232    31687.822320     0.3
Spread Q Bspline              83712.418560   167424.837120     1.4
Gather F Bspline              83712.418560  1004549.022720     8.2
3D-FFT                       263902.919508  2111223.356064    17.1
Solve PME                      4287.521437   274401.372000     2.2
NS-Pairs                      10955.692493   230069.542353     1.9
Reset In Box                    261.606540     2354.458860     0.0
Shift-X                        2616.013080    15696.078480     0.1
CG-CoM                           87.202180     2528.863220     0.0
Virial                         1313.406567    23641.318206     0.2
Update                         1308.006540    40548.202740     0.3
Stop-CM                        1308.000000    13080.000000     0.1
P-Coupling                     1308.006540     7848.039240     0.1
Calc-Ekin                      1308.013080    35316.353160     0.3
Constraint-V                   1308.006540     7848.039240     0.1
Constraint-Vir                 1308.019620    31392.470880     0.3
Settle                          436.006540   140830.112420     1.1
-----------------------------------------------------------------------
Total                                      12322777.937807   100.0
-----------------------------------------------------------------------
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