GROMACS version: 2023.1
GROMACS modification: No
Hello.
I run 100 ns MD of Ionic Liquids with GAFF.
The value of density I got deviated by about 3 % from Experiment.
Could one take a look at my production .mdp file and suggest some changes for improving my result as I try hard and hard but no improvement.
See the file below:
title = MD equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000000 ; 2 * 50000000 = 100000 ps (100 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps nstxout-compressed = 500 ; save compressed coordinates every 1.0 ps compressed-x-grps = System ; save the whole system ; remove drifts of the center of mass comm-mode = linear ; remove COM translation nstcomm = 10 ; number of steps for COM removal comm-grps = System ; COM translation removed from system ; Bond parameters continuation = yes ; Restarting after NPT constraint_algorithm = lincs ; holonomic constraints lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ;ns_type = grid ; search neighboring grid cells nstlist = 20 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation coulomb-modifier = Potential-shift-Verlet ; shifts potential by constant so potential is 0 at cut-off fourierspacing = 0.168 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 1.0 ; time constant, in ps ref_t = 333.15 ; reference temperature, one for each group, in K nsttcouple = 1 ; frequency to couple temperature ; Pressure coupling is on pcoupl = C-rescale ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 4.0 ; time constant, in ps ref_p = 1.01 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 nstpcouple = 1 ; frequency to couple pressure ;refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; Velocity generation is off
Thank You.