Hi All <br><br>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. <br>Simulation was done at 298K and 1bar and usual procedure for generating a water box and equilibration were used.
<br><br>Average interaction energy reported in the log file was <br> Epot (kJ/mol) Coul-SR LJ-SR <br> WAT-rest -8.13828e+01 1.21886e+01<br><br>giving a total of -8.13828e+01 + 1.21886e+01
= -69.194 kJ/mol <br><br>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. <br><br>any clues on origin of this discrepancy ? relevant .top , .mdp files are below.
<br><br>Thanks<br>Sandeep <br><br><br>;-----------------------<br><b>;MD.MDP for bulk TIP3P </b><br>;-----------------------<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md
<br>tinit = 0.0<br>dt = 0.002 <br>nsteps = 200000 ; 400 ps <br>nstcomm = 1<br>nstxout = 50 <br>nstlog = 50<br>nstenergy = 50
<br>nstxtcout = 50 <br>nstlist = 5<br>energygrps = WAT<br>ns_type = grid<br>;PME<br>coulombtype = PME<br>rlist = 0.9<br>rcoulomb = 0.9<br>
rvdw = 0.9<br>fourierspacing = 0.12<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Temperature coupling <br>Tcoupl = berendsen<br>tc-grps = SOL WAT
<br>tau_t = 0.1 0.1 <br>ref_t = 298 298 <br>; Pressure coupling is on<br>Pcoupl = berendsen <br>Pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility =
4.5e-5<br>ref_p = 1.0<br>;-----------------------<br><b>; TOP FILE FOR TIP3P BULK </b><br>; Include forcefield parameters<br>#include "ffoplsaa.itp"<br>; Include water topology<br>#include "tip3p.itp
"<br>[ system ]<br>; Name<br>bulk water<br>[ molecules ]<br>; Compound #mols<br>SOL 2180 <br>----------------------<br><br><b>bits of log file from production run:</b><br><br> <====== ############### ==>
<br> <==== A V E R A G E S ====><br> <== ############### ======><br><br> Energies (kJ/mol)<br> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.<br> 1.35174e+04 -
8.91571e+04 -1.10392e+04 -8.66790e+04 1.61998e+04<br> Total Energy Temperature Pressure (bar)<br> -7.04792e+04 2.97985e+02 2.27514e+00<br><br> Box-X Box-Y Box-Z Volume Density (SI)
<br> 4.06327e+00 4.06327e+00 4.06327e+00 6.70858e+01 9.72133e+02<br> pV<br> 9.03527e+00<br><br> Total Virial (kJ/mol)<br> 5.40366e+03 -6.97436e+00 2.78681e+00<br> -6.97436e+00
5.38940e+03 -2.37439e+00<br> 2.78681e+00 -2.37439e+00 5.39318e+03<br><br> Pressure (bar)<br> -2.28378e+00 3.27978e+00 -1.13390e+00<br> 3.27978e+00 4.65423e+00 1.52221e+00<br> -1.13390e+00
1.52221e+00 4.45496e+00<br><br> Total Dipole (Debye)<br> 3.23351e+00 -1.12569e+01 1.42062e+01<br><br> Epot (kJ/mol) Coul-SR LJ-SR <br> WAT-WAT 0.00000e+00 0.00000e+00<br> WAT-rest -
8.13828e+01 1.21886e+01<br> rest-rest -8.90758e+04 1.35052e+04<br><br> T-SOL T-WAT<br> 2.97985e+02 2.97422e+02<br><br><br> M E G A - F L O P S A C C O U N T I N G<br><br> RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
<br> T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)<br> NF=No Forces<br><br> Computing: M-Number M-Flops % of Flops<br>-----------------------------------------------------------------------
<br> Coul(T) + LJ [W3-W3] 21419.733112 8182338.048784 66.4<br> Outer nonbonded loop 3168.782232 31687.822320 0.3<br> Spread Q Bspline 83712.418560 167424.837120 1.4<br> Gather F Bspline
83712.418560 1004549.022720 8.2<br> 3D-FFT 263902.919508 2111223.356064 17.1<br> Solve PME 4287.521437 274401.372000 2.2<br> NS-Pairs 10955.692493
230069.542353 1.9<br> Reset In Box 261.606540 2354.458860 0.0<br> Shift-X 2616.013080 15696.078480 0.1<br> CG-CoM 87.202180 2528.863220
0.0<br> Virial 1313.406567 23641.318206 0.2<br> Update 1308.006540 40548.202740 0.3<br> Stop-CM 1308.000000 13080.000000 0.1
<br> P-Coupling 1308.006540 7848.039240 0.1<br> Calc-Ekin 1308.013080 35316.353160 0.3<br> Constraint-V 1308.006540 7848.039240 0.1<br> Constraint-Vir
1308.019620 31392.470880 0.3<br> Settle 436.006540 140830.112420 1.1<br>-----------------------------------------------------------------------<br> Total
12322777.937807 100.0<br>-----------------------------------------------------------------------<br><br><br><br><br><br><br><br><br><br>