[gmx-users] Inconsistence of SPC/E and TIP4P water in Gromacs

[Mark Abraham]

Hi,

On Thu, May 11, 2017 at 3:31 AM ZUO Taisen <zuots at ihep.ac.cn> wrote:

>
> 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.
>

We shouldn't have a mailing list where thousands of recipients can receive
large emails :-)


> I'm eager to know why! Thank you very much!
>

Force fields, including water models, are parameterized to reproduce
certain theoretical or experimental data. To the extent that those targets
resemble other observables, you might expect agreement. You should expect
the level of such agreement to differ between models.

Mark


> 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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