Sample MDP file for All-atom Structure-based simulations in Gromacs v4

;For more information on these variables, see the gromacs manual.
;Run control: Use Langevin dynamics.
integrator = sd
;time step in reduced units.
dt = 0.0005
;number of integration steps
nsteps = 100000
;frequency to write coordinates to output trajectory .trr file ; .trr files are used to continue runs. Unless you are interested in velocities, ; you don't need to save data to the .trr file too often.
nstxout = 100000
;frequency to write velocities to output trajectory .trr file
nstvout = 100000
;frequency to write energies to log file
nstlog = 1000
;frequency to write energies to energy file ; after you run your simulation, use the g_energy module of gromacs to extract each term
nstenergy = 1000
;frequency to write coordinates to .xtc trajectory
nstxtcout = 1000
;group(s) to write to .xtc trajectory.
;NOTE: Group name "system" is defined if you are NOT using an index file. If you use an index file, all group references need to be consistent with the names given in the index file. Our webpage, by default, names the chains "1", "2", ... You can change these names to whatever you like, just make sure the mdp file uses the same naming scheme. For more information on group usage, please consult the Gromacs manual.
xtc_grps = system
;group(s) to write to energy file ; "system" indicates that the energy of the entire system will be written to the energy file.
energygrps = system
;Frequency to update the neighbor list (and the long-range forces,
;when using twin-range cut-off's).
nstlist = 20
coulombtype = Cut-off
;Make a grid in the box and only check atoms in neighboring grid cells
;when constructing a new neighbor list every nstlist steps.
ns_type = grid
;cut-off distance for the short-range neighbor list (NOTE: cut-offs should be longer if running a CA model)
rlist = 1.5
;treatment of electrostatic interactions
rcoulomb = 1.5
;treatment of van der waals interactions
rvdw = 1.5
; Periodic boundary conditions in all the directions
pbc = xyz
periodic_molecules = yes
table-extension = 20 ; (nm) !IMPORTANT! Set this so that rvdw + table-extension equals half of the box's longest diagonal.
;Temperature coupling
tc-grps = system
tau_t = 1.0 ; Temperature coupling time constant. Smaller values = stronger coupling.
ref_t = 50.0 ; In reduced units (see Gromacs Manual for explanation. We find many proteins fold around T=100-120)
;Pressure coupling
Pcoupl = no
;Velocity generation
gen_vel = yes
gen_temp = 50.0
gen_seed = 30
ld_seed = 130
comm_mode = angular ; center of mass velocity removal. Make sure you select what is proper for your simulation.
;NOTE on comm_mode: When using periodic boundary conditions, which improves the speed of neighbor searching (in Gromacs V 4.0.X), removing the angular velocity will lead to a warning at the grompp stage of simulations. So long as the box size is properly sized, such that your system does not cross the boundaries during the simulation, then this warning is harmless and you can simply issue -maxwarn X, where X is the number of allowed warning messages.