# Appropriate .mdp settings for Gromos54a7

**URL:** <https://gromacs.bioexcel.eu/t/appropriate-mdp-settings-for-gromos54a7/4667>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [August 24, 2022, 6:54am UTC](https://gromacs.bioexcel.eu/t/appropriate-mdp-settings-for-gromos54a7/4667 "2022-08-24T06:54:09Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![Joseph](https://avatars.discourse-cdn.com/v4/letter/j/dc4da7/32.png) [@Joseph](https://gromacs.bioexcel.eu/u/Joseph)\
**Post date:** [August 24, 2022, 6:54am UTC](https://gromacs.bioexcel.eu/t/appropriate-mdp-settings-for-gromos54a7/4667/1 "2022-08-24T06:54:09Z")

</div>

GROMACS version: 2020.1  
GROMACS modification: No

Are there any particular issues you notice with the following md.mdp file for Gromos54a7 simulations:

title = Gromos MD simulation  
; Run parameters  
integrator = md ; leap-frog integrator  
nsteps = 100000000 ; 200 ns (1 ns)  
dt = 0.002 ; 2 fs  
; Output control  
nstxout = 0 ; save coordinates every 10.0 ps  
nstvout = 0 ; save velocities every 10.0 ps  
nstenergy = 5000 ; save energies every 10.0 ps  
nstlog = 5000 ; update log file every 10.0 ps  
nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps  
; nstxout-compressed replaces nstxtcout  
compressed-x-grps = System ; replaces xtc-grps  
; Bond parameters  
continuation = yes ; Restarting after NPT  
constraint\_algorithm = lincs ; holonomic constraints  
constraints = all-bonds ; all 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 = 1.4 ; short-range electrostatic cutoff (in nm)  
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)  
; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
; Temperature coupling is on  
tcoupl = V-rescale ; modified Berendsen thermostat  
tc-grps = Protein Non-Protein ; two coupling groups - more accurate  
tau\_t = 0.1 0.1 ; time constant, in ps  
ref\_t = 300 300 ; 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