# Minimization of a membrane-peptide complex **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters, mdrun, simulation-setup\ **Created:** [August 2, 2025, 3:54pm UTC](https://gromacs.bioexcel.eu/t/minimization-of-a-membrane-peptide-complex/12477 "2025-08-02T15:54:59Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![tanjim\_ibl](https://avatars.discourse-cdn.com/v4/letter/t/d78d45/32.png) [@tanjim\_ibl](https://gromacs.bioexcel.eu/u/tanjim_ibl)\ **Post date:** [August 2, 2025, 3:54pm UTC](https://gromacs.bioexcel.eu/t/minimization-of-a-membrane-peptide-complex/12477/1 "2025-08-02T15:54:59Z")
GROMACS version:2025.2 GROMACS modification: No When I use this mdp to neutralize the system I am getting some notes. **minim.mdp:** ; ions.mdp - used as input into grompp to generate ions.tpr integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 nstlist = 1 ; cutoff-scheme = Verlet ns\_type = grid coulombtype = cutoff rcoulomb = 1.2 rvdw = 1.2 pbc = xyz **Outputs:** Command line: gmx grompp -f minim.mdp -o minim.tpr -c solv.gro -p topol.top -n index.ndx Ignoring obsolete mdp entry ‘ns\_type’ NOTE 1 [file minim.mdp]: With Verlet lists the optimal nstlist is \>= 10, with GPUs \>= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -281059331 Generated 167799 of the 167910 non-bonded parameter combinations Generating 1-4 interactions: fudge = 1 Generated 117432 of the 167910 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘POPG’ Excluding 3 bonded neighbours molecule type ‘DCLE’ Excluding 3 bonded neighbours molecule type ‘Protein’ Excluding 2 bonded neighbours molecule type ‘SOL’ NOTE 2 [file topol.top, line 25]: System has non-zero total charge: -388.000000 Total charge should normally be an integer. > **[Floating point arithmetic - GROMACS 2025.2 documentation](https://manual.gromacs.org/current/user-guide/floating-point.html)** for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 473517.00 The integrator does not provide a ensemble temperature, there is no system ensemble temperature NOTE 3 [file minim.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. But it works. Then I run energy minimization after this with this mdp: integrator = steep emtol = 1000.0 nsteps = 5000 nstlist = 10 cutoff-scheme = Verlet rlist = 1.2 vdwtype = Cut-off vdw-modifier = Force-switch rvdw\_switch = 1.0 rvdw = 1.2 coulombtype = PME rcoulomb = 1.2 ; constraints = h-bonds constraint\_algorithm = LINCS Then I get some errors while running _gmx grompp -f ions.mdp -o neutral.tpr -c neutral.gro -p topol.top -n index.ndx gmx mdrun -v -deffnm neutral_ **And these were in the results, although the system converged to the desired steepest descent.** step 18: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Step 34, time 0.034 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000066, max 0.010883 (between atoms 7281 and 7280) bonds that rotated more than 30 degrees: ![1](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/1/11f8b71bdb8286944536eabdfb84baf6180c5515.png) atom 1 atom 2 angle previous, current, constraint length 7282 7280 35.2 0.1110 0.1108 0.1111