# Improving MD Results Accuracy **URL:** \ **Category:** User discussions\ **Created:** [December 2, 2023, 1:32pm UTC](https://gromacs.bioexcel.eu/t/improving-md-results-accuracy/7773 "2023-12-02T13:32:41Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [December 2, 2023, 1:32pm UTC](https://gromacs.bioexcel.eu/t/improving-md-results-accuracy/7773/1 "2023-12-02T13:32:41Z")
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. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [December 7, 2023, 2:41pm UTC](https://gromacs.bioexcel.eu/t/improving-md-results-accuracy/7773/2 "2023-12-07T14:41:46Z")
The issue is more likely tied to the topology of the molecules in the system rather than `.mdp` settings. A 3% deviation isn’t terrible, usually a 2% deviation is an acceptable tolerance when validating parameters. ---
**Author:** ![umar](https://avatars.discourse-cdn.com/v4/letter/u/59ef9b/32.png) [@umar](https://gromacs.bioexcel.eu/u/umar)\ **Post date:** [December 8, 2023, 3:36am UTC](https://gromacs.bioexcel.eu/t/improving-md-results-accuracy/7773/3 "2023-12-08T03:36:27Z")
Thank You, Sir.