Help my .mdp file for simulation of carbohydrates

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1

GROMACS version:
GROMACS modification: Yes/No
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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

2

This is an obsolete setting.

Flexible water is rarely beneficial.

Does your force field use constraints? Nearly all do, at least for bonds involving H. Which force field are you using for your simulations?

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.

nstlist should always be 1 for EM.

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.

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.

4

That one is straight from my tutorial that uses OPLS, so yes, I’d endorse it as being adequate for energy minimization :)

5

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

6

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” :)

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