Talk:Mod:Hunt Research Group/gromacs control MD
From ChemWiki
example input
;run control integrator = md dt = 0.001 nsteps = 10000 ;output control nstlog = 100 nstenergy = 100 nstxout-compressed = 100 ;neighbor control cutoff-scheme = Verlet pbc = xyz nstlist =5 ns_type =grid ;electrostatics and vdw coulombtype = PME rcoulomb = 1.2 ewald-rtol = 1.0e-5 fourierspacing = 0.06 pme-order = 8 vdwtype = Cut-off rvdw = 1.2 DispCorr = EnerPres ;temperature tcoupl = V-rescale tc-grps = System tau-t = 0.1 ref-t = 400.0 ;presure pcoupl = Berendsen pcoupltype = isotropic tau-p = 1.0 ref-p = 1.0 compressibility = 4.5e-5 ; refcoord_scaling = com ;generate velocities gen-vel = yes gen-temp = 400 gen-seed = -1 ;bond constraints constraints = h-bonds constraint-algorithm = LINCS continuation = no
description
integrator = md # use leap-frog, note velocity verlet md-vv is avialable dt = 0.001 # time step in ps, so 0.001 is 1 femto second nsteps = 10000 # the number of steps so 0.001*10000=10ps nstlog = 1000 # energies written to file every x steps to log file nstenergy = 1000 # energies written to file every x steps to energy file nstxout-compressed = 100 # coords written every x steps using compression, produces the *.xtc file cutoff-scheme = Verlet #use pair list buffering nstlist =5 #frequency to updare neighbor list, this is a minimum and verlet may increase this #nstlist can affect the accuracy of your simulation ns-type =grid #make a grid in the box and only check atoms in the neighboring grid cells when updating pbc = xyz #periodic boundary conditions in all directions coulombtype = PME # fast smooth particle-mesh Ewald electrostatics rcoulomb = 1.2 # distance for the Coulomb cut-off ewald-rtol = 1.0e-5 #relative strength of Ewald-shifted direct potential at rcoulomb fourierspacing = 0.06 # 0.12 standard pme-order = 8 # interpolation order for PME, 4=cubic vdwtype = Cut-off # use a plain cut-off with pair list radius rvdw = 1.2 # VdW cut-off in nm DispCorr = EnerPres # apply long range dispersion corrections for energy and pressure tcoupl = V-rescale # temperture coupling with velocity rescaling and a stochastic term tc-grps = System # groups to coluple to seperate temperature baths tau-t = 0.1 time constant for coupling in ps ref-t = 300.0 reference temperature in K pcoupl = Berendsen # exponential relazation pressure coupling pcoupltype = isotropic # isotropic pressure coupling tau-p = 1.0 #time constant for coupling in ps ref-p = 1.0 #reference pressure in bar compressibility = 4.5e-5 # compressibility in bar-1, this is the value for water ; refcoord_scaling = com # scale the position of the CoM for each molecule, don't scale atom coord to CoM? gen-vel = yes # generate velocities according to Maxwell distribution gen-temp = 300 # temperature for Maxwell distribution gen-seed = -1 # initalize random number generator constraints = h-bonds # bonds with H atoms are constrained constraint-algorithm = LINCS # constraint method, SHAKE is slightly slower and less stable continuation = no # apply constraints to the starting configuration <pre>
