Dear Gromacs users,I am doing a simulation on CO2/water interface. Two separate simulations (NPT) have been done sucessfully for pure CO2 and pure water systems. Then two CO2 gro files and one water gro files were connected into one single gro files for CO2/water interface (CO2/water/CO2).
The CO2/water system was simulated in NVT ensemble first with water molecules fixed in positions for 500ps, and then the position constraints were removed and further 500ps simulation run were made. The temperature were coupled with v-rescale method and the average value was exactly the same as the target temperature. The CO2/water system was further simulated in NPT ensemble for 3000ps, but the result seems quite bad. The average values of temperature and pressure are 344.7K and -6.89249e+02 bar, respectively, which are quite different from the targets.
The reason may be that the system is far from equilibrium, but the simulation time for 3ns is enough for my opinion.
I would be grateful if anyone could give me some advice. The .mdp file is listed as follows.
title = chcwaaa
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; run control
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
integrator = md ;a leap-frog integrator for integrating Newton's equations of motion
tinit = 0 ; default, starting time for your run
dt = 0.001 ; time step for integration, default 0.001 ps
nsteps = 3000000 ; maximum number of steps to integrate or minimize, -1 is no maximum
init-step = 0 ; the starting step. t=tinit + dt(init-step + i)
comm-mode = Linear ; remove center of mass translation; Angular: remove center of mass translation and rotation around the center of mass
nstcomm = 100 ; frequency for center of mass motion removal
comm-grps = system ; groups for center of mass motion removal, default is the whole system
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; output control
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
nstxout = 5000 ; frequency to write coordinates to output trajectory file, the last coordinates are always written
nstvout = 5000 ; frequency to write velocities to output trajectory
nstfout = 0 ; frequency to write forces to output trajectory
nstlog = 5000 ; frequency to write energies to log file
nstcalcenergy = 100 ; default, frequency for calculating energies.
nstenergy = 300 ; frequency to write energies to energy file, should be a multiple of nstcalcenergy
nstxtcout = 300 ; frequency to write coordinates to xtc trajectory
xtc-precision = 1000 ; precision to write to xtc trajectory, default
xtc-grps = system ; default the whole system
energygrps = system ; groups to write to energy file
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; neighbor searching
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
cutoff-scheme = Verlet ; generate a pair list with buffering.
nstlist = 10 ; default, frequency to update the neighbor list
ns-type = grid ; make a grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list.
pbc = xyz
periodic-molecules = no ; molecules are finite, default
verlet-buffer-drift = 0.005 ; This sets the target energy drift per particle caused by the Verlet buffer, which indirectly sets rlist.
rlist = 1 ; With cutoff-scheme=Verlet, this is by default set by the verlet-buffer-drift option and the value of rlist is ignored
nstcalclr = 1
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; electrostatics
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
coulombtype = PME ;Fast smooth Particle-Mesh Ewald (SPME) electrostatics
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1.6 ;distance for the Coulomb cut-off
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; vdw
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
vdwtype = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw = 1.6
DispCorr = EnerPres ;apply long range dispersion corrections for Energy and Pressure
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Ewald
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
fourierspacing = 0.12 ;
pme-order = 4
ewald-rtol = 1e-5
ewald-geometry = 3d
optimize-fft = yes ;Calculate the optimal FFT plan for the grid at startup. This saves a few percent for long simulations, but takes a couple of minutes at start.
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Temperature coupling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
tcoupl = v-rescale
tc-grps = system
tau-t = 0.1 ; time constant for coupling (one for each group in tc-grps), -1 means no temperature coupling
ref-t = 323 ; reference temperature for coupling (one for each group in tc-grps)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Pressure coupling
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;Pcoupl = Parrinello-Rahman ; to equilibrium using berendsen, to product using Parrinello-Rahman
pcoupltype = semiisotropic
nstpcouple = -1 ; default,The default value of -1 sets nstpcouple equal to nstlist, unless nstlist ≤0, then a value of 10 is used
tau-p = 2.0 ; time constant for coupling
compressibility = 0 4.5e-5
ref-p = 200.0 200.0;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; velocity generation
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Bonds
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
constraints = none
constraint-algorithm = SHAKE
shake-tol = 0.0001
--
Best wishes,Cong Chen********************************************************************************************Dr. Cong ChenAssociate ProfessorKey Laboratory of Ocean Energy Utilization and Energy Conservation of Ministry of EducationSchool of Energy and Power EngineeringDalian University of TechnologyLingGong Road 2, Dalian, Liaoning Province, 116024, P. R. ChinaTel: 86-411-84708774Mobile: 86-15840897865Website:
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
