# Help my .mdp file for simulation of carbohydrates **URL:** \ **Category:** User discussions\ **Created:** [August 10, 2020, 12:47pm UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648 "2020-08-10T12:47:09Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![protonsantosh](https://avatars.discourse-cdn.com/v4/letter/p/c6cbf5/32.png) [@protonsantosh](https://gromacs.bioexcel.eu/u/protonsantosh)\ **Post date:** [August 10, 2020, 12:47pm UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648/1 "2020-08-10T12:47:09Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Dear altruist, here I am trying to run simulation for finding diffusion coefficient for carbohydrates . Is my .mdp file good for simulation? em.mdp cpp = /lib/cpp define = -DFLEX\_SPCE constraints = none integrator = steep ; steepest descent method nsteps = 50000000 ; total number of steps ; ; Energy minimizing stuff ; emtol = 50 ; force tolerance (KJ mol^-1 nm^-1) emstep = 0.002 ; initial step size (nm) nstcomm = 1 ; frequency for central of mass motion removal ns\_type = grid ; neighbour searching type nstlist = 10000 rlist = 1.0 ; cut off distance for the short range neighbor list (nm) coulombtype = PME rcoulomb = 1.0 ; Coulomb cut off rvdw = 1.0 ; vanderwaals cut off nstxtcout = 20 Tcoupl = no Pcoupl = no gen\_vel = no ---
**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:** [August 10, 2020, 4:46pm UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648/2 "2020-08-10T16:46:44Z")
> [@protonsantosh](#): > > cpp = /lib/cpp This is an obsolete setting. > [@protonsantosh](#): > > define = -DFLEX\_SPCE Flexible water is rarely beneficial. > [@protonsantosh](#): > > constraints = none Does your force field use constraints? Nearly all do, at least for bonds involving H. Which force field are you using for your simulations? > [@protonsantosh](#): > > emstep = 0.002 ; initial step size (nm) This is a rather small initial step size, so your EM may take a long time to complete. The default value of 0.02 is typically fine. > [@protonsantosh](#): > > nstlist = 10000 `nstlist` should always be 1 for EM. > [@protonsantosh](#): > > rlist = 1.0 ; cut off distance for the short range neighbor list (nm) > coulombtype = PME > rcoulomb = 1.0 ; Coulomb cut off > rvdw = 1.0 ; vanderwaals cut off Nonbonded settings depend on the force field being used, so these should be adjusted if your force field requires different cutoffs, potential or force switching, etc. > [@protonsantosh](#): > > nstxtcout = 20 One rarely writes XTC files during EM. There’s not much of a point in writing trajectories anyway, since the frame interval will be uneven, therefore most programs can’t read them. ---
**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:** [August 11, 2020, 1:03am UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648/4 "2020-08-11T01:03:09Z")
That one is straight from my tutorial that uses OPLS, so yes, I’d endorse it as being adequate for energy minimization :) ---
**Author:** ![protonsantosh](https://avatars.discourse-cdn.com/v4/letter/p/c6cbf5/32.png) [@protonsantosh](https://gromacs.bioexcel.eu/u/protonsantosh)\ **Post date:** [August 11, 2020, 12:05pm UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648/5 "2020-08-11T12:05:34Z")
Professor, thank you for prompt reply and thats quite helpful. I wonder if these NVT.mdp file and equilibration.mdp file are compatible with the system. ``` NVT.mdp ``` ;PREPROCESSING parameters (NVT) tinit = 0 integrator = md dt = 0.002 nsteps = 50000000 nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 1000 nstvout = 1000 nstfout = 1000 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns\_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. vdwtype = cut-off coulombtype = PME fourierspacing = 0.12 ; grid spacing for FFT pme-order = 4 ewald-rtol = 1e-05 rcoulomb = 1.0 rvdw = 1.0 epsilon-r = 1.0 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = v-rescale tc-grps = system tau\_t = 0.01 ref\_t = 312.15 ;PRESSURE COUPLING is on Pcoupl = no ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 298.14 gen\_vel = no; ; generate initially gen\_temp = 312.15 gen\_seed = 173504 ;give different values for different trials. ld\_seed = 1993 ;BONDS parameters constraints = all-bonds pbc = xyz ;SIMULATED ANNEALING parameters are not specified. ``` Equilibration.mdp ``` ; ;PREPROCESSING parameters cpp = /lib/cpp integrator = md ; leap-frog integrator dt = 0.002 ; 2.0 fs nsteps = 50000000 ; 0.002\*50000000 = 100000 ns nstcomm = 1 ;OUPUT CONTROL parameters. nstxout = 1000 ;save coordinates every 2.0 ps nstvout = 1000 ;save velocities every 2.0 ps nstfout = 1000 ;save forces every 2.0 ps nstlog = 1000 ;update log file every 2.0 ps nstenergy = 1000 ;save energies every 2.0 ps nstxtcout = 1000 energygrps = system ;NEIGHBOUR SEARCHING parameters. nstlist = 10 ns\_type = grid rlist = 1.0 ;ELECTROSTATIC and VdW parameters. vdwtype = cut-off coulombtype = PME ; Particle Mesh Ewald for long-range fourierspacing = 0.12 ; grid spacing for FFT pme-order = 4 ewald-rtol = 1e-05 rcoulomb = 1.0 rvdw = 1.0 epsilon-r = 1.0 ;BERENDSEN TEMPERATURE COUPLING is on in two groups Tcoupl = v-rescale ; modified Berendsen thermostat tc-grps = system tau\_t = 0.01 ; time constant, in ps ref\_t = 312.15 ; reference temperature, in K ;PRESSURE COUPLING is on Pcoupl = berendsen tau\_p = 0.8 ; time constant, in ps compressibility = 4.6e-5 ; isothermal compressibility of water, bar^-1 ref\_p = 1.0 ; reference pressure, in bar ;SIMULATED ANNEALING parameters are not specified. ;GENERATE VELOCITIES is on at 293.2K gen\_vel = yes ; generate initially gen\_temp = 312.15 gen\_seed = 173504 ;give different values for different trials. ld\_seed = 1993 ;BONDS parameters constraints = all-bonds unconstrained-start = no pbc = xyz ; 3-D PBC ---
**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:** [August 11, 2020, 5:10pm UTC](https://gromacs.bioexcel.eu/t/help-my-mdp-file-for-simulation-of-carbohydrates/648/6 "2020-08-11T17:10:46Z")
As before, you have a lot of outdated keywords. Beware using Berendsen methods for temperature or pressure - they should only be used for initial equilibration; their distributions are demonstrably incorrect. It would be helpful if you asked more specific questions rather than a blanket request that is akin to “please check my work” :)