Hi guys:
I have compared the SPC/E and TIP4P water of the opls force field in
Gromacs.But there is something inconsistent of the potential energy in the
system
The potential energy of SPC/E water is -4.71400e+04/1000=-47.14kJ/mol which is
far from the results from literature (Peter G. Kusalik,
Science,vol,265,26,p1219-1221,1994)
The potential energy TIP4P water is -4.17875e+04/1000=41.787kJ/mol which is
very close to the literature -41.8kJ/mol(Peter G. Kusalik,
Science,vol,265,26,p1219-1221,1994)
I have attached all the files simulating the SPC/E and TIP4P water(.trr .xtc
files are delected) and also the related paper in my last email but was
suspended because of the files were too big.So no files was attached this time
but the .mdp file was posted as following.
I'm eager to know why! Thank you very much!
TIP4P simulation results:
Statistics over 30000001 steps using 300001 frames
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
7.71821e+03 -2.05973e+02 -4.93956e+04 9.58136e+01
-4.17875e+04
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
7.30494e+03 -3.44826e+04 2.93006e+02 -1.14009e+02 1.41117e+00
SPC/E simulation results:
Statistics over 30000001 steps using 300001 frames
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
9.23352e+03 -2.12206e+02 -5.62576e+04 9.63633e+01 -4.71400e+04
Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar)
7.30494e+03 -3.98350e+04 2.93005e+02 -1.18040e+02 1.64654e+00
title= OPLS MD waterethanol siimulation
; Run parameters
integrator= md; leap-frog integrator
nsteps= 30000000; 1 * 20000000 = 20000 ps (20 ns)
dt = 0.001; 1 fs
; Output control
nstxout = 100000; save coordinates every 10.0 ps
nstvout = 100000; save velocities every 10.0 ps
nstenergy = 100000; save energies every 10.0 ps
nstlog = 100000; update log file every 10.0 ps
nstxout-compressed = 100000 ; save compressed coordinates every 10.0 ps
define =-DEFLEXIBLE ; flexible water
compressed-x-grps = System ; replaces xtc-grps
; Bond parameters
continuation = yes; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = none; H bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme
rcoulomb = 1.2; short-range electrostatic cutoff (in nm)
rvdw = 1.2; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing= 0.12; grid spacing for FFT
; Temperature coupling is on
tcoupl= V-rescale ; modified Berendsen thermostat
tc-grps= SOL ; two coupling groups - more accurate
tau_t= 0.1 ; time constant, in ps
ref_t= 293 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water,
bar^-1
; Periodic boundary conditions
pbc= xyz; 3-D PBC
; Dispersion correction
DispCorr= EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel= no; Velocity generation is off
--
Taisen Zuo
China Spallation Neutron Source，Institute of High Energy Physics， Chinese
Academy of Science
A1-510, Zhongziyuan road NO.1, Dongguan, Guangdong, PR China. 523770
Tel: 86-0769-89156495
Cell: 13650469795
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