[gmx-users] interaction energy of bulk TIP3P
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+011.21886e+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 = 20 ; 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. PotentialKinetic En.
1.35174e+04 -8.91571e+04 -1.10392e+04 -8.66790e+041.61998e+04
Total EnergyTemperature Pressure (bar)
-7.04792e+042.97985e+022.27514e+00
Box-X Box-Y Box-Z Volume Density (SI)
4.06327e+004.06327e+004.06327e+006.70858e+019.72133e+02
pV
9.03527e+00
Total Virial (kJ/mol)
5.40366e+03 -6.97436e+002.78681e+00
-6.97436e+005.38940e+03 -2.37439e+00
2.78681e+00 -2.37439e+005.39318e+03
Pressure (bar)
-2.28378e+003.27978e+00 -1.13390e+00
3.27978e+004.65423e+001.52221e+00
-1.13390e+001.52221e+004.45496e+00
Total Dipole (Debye)
3.23351e+00 -1.12569e+011.42062e+01
Epot (kJ/mol)Coul-SR LJ-SR
WAT-WAT0.0e+000.0e+00
WAT-rest -8.13828e+011.21886e+01
rest-rest -8.90758e+041.35052e+04
T-SOL T-WAT
2.97985e+022.97422e+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=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
NF=No Forces
Computing:M-Number M-Flops % of Flops
---
Coul(T) + LJ [W3-W3] 21419.733112 8182338.04878466.4
Outer nonbonded loop 3168.78223231687.822320 0.3
Spread Q Bspline 83712.418560 167424.837120 1.4
Gather F Bspline 83712.418560 1004549.022720 8.2
3D-FFT 263902.919508 2111223.35606417.1
Solve PME 4287.521437 274401.372000 2.2
NS-Pairs 10955.692493 230069.542353 1.9
Reset In Box261.606540 2354.458860 0.0
Shift-X2616.01308015696.078480 0.1
CG-CoM 87.202180 2528.863220 0.0
Virial 1313.40656723641.318206 0.2
Update 1308.00654040548.202740 0.3
Stop-CM1308.0013080.00 0.1
P-Coupling 1308.006540 7848.039240 0.1
Calc-Ekin 1308.01308035316.353160 0.3
Constraint-V 1308.006540 7848.039240 0.1
Constraint-Vir 1308.01962031392.470880 0.3
Settle 436.006540 140830.112420 1.1
---
Total 12322777.937807 100.0
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Re: [gmx-users] interaction energy of bulk TIP3P
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+011.21886e+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. The PME algorithm does an approximation to the full periodic Coulomb summation, but does so with a calculation in direct space, as above, and another in reciprocal space, where your energy groups are not meaningful. So you're only getting the direct-space component of the interaction energy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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