Use LINCS instead of SHAKE
; md-continue.mdp
; 5.0 ps NVT production with Langevin thermostat
-#################################### INPUT ####################################
+#################################### INPUT #####################################
ld_seed = RAND ; Use random seed from WESTPA
-################################# INTEGRATOR ##################################
+################################# INTEGRATOR ###################################
integrator = sd ; Langevin thermostat
dt = 0.002 ; Timestep (ps)
nsteps = 2500 ; Simulation duration (timesteps)
nstcomm = 500 ; Center of mass motion removal interval
comm_mode = linear ; Center of mass motion removal mode
-################################## ENSEMBLE ###################################
+comm-grps = system ; Remove center of mass motion of system
+################################## ENSEMBLE ####################################
ref_t = 300 ; System temperature (K)
tau_t = 1.0 ; Thermostat time constant (ps)
-tc_grps = system ; Apply thermostat to complete system
-########################### NONBONDED INTERACTIONS ############################
-cutoff_scheme = group ; Method of managing neighbor lists
-pbc = xyz ; Use periodic boundary conditions
-coulombtype = PME ; Calculate coulomb interactions using PME
-rcoulomb = 1.0 ; Coulomb cutoff of infinity
-vdw_type = cut-off ; Calculate van der Waals interactions using cutoff
-vmd-modifier = force-switch
-rvdw-switch = 0.8 ; Start switching vdW interactions off at .8 nm
-rvdw = 0.9 ; Van der Waals interactions off at .9 nm
-rlist = 0.0 ; Neighbor list cutoff
-nstlist = 10 ; Do not update neighbor list
-DispCorr = yes ; Use a long-range analytical dispersion correction
-################################### OUTPUT ####################################
+tc_grps = Protein Non-Protein ; Apply thermostat to system
+continuation = yes
+############################ BONDED INTERACTIONS ###############################
+constraints = hbonds ; Constrain bonds to hydrogen atoms
+constraint_algorithm = LINCS ; Constrain bonds using LINCS
+########################### NONBONDED INTERACTIONS #############################
+coulombtype = PME ; Switch/PME long-range electrostatics
+fourierspacing = 0.1 ; spacing for PME grid
+pme_order = 6 ; Interpolation order for PME
+ewald_rtol = 0.000001
+pbc = xyz ; Periodic boundary condition
+rcoulomb = 1.0 ; Short-range electrostatic cutoff (nm)
+rcoulomb_switch = 0.9 ; Short-range electrostatic switch cutoff (nm)
+vdwtype = Switch ; Switch van der Waals interactions
+rvdw = 0.9 ; Van der Waals cutoff (nm)
+rvdw_switch = 0.8 ; Van der Waals switch cutoff (nm)
+DispCorr = Ener ; Long-range dispersion correction to energy
+ns_type = grid ; Update neighbor list using grid
+nstlist = 10 ; Neighbor list update interval (timesteps)
+rlist = 1.00 ; Neighbor list cut-off (nm)
+cutoff-scheme = group ; Cutoff scheme
+################################### OUTPUT #####################################
nstlog = 50 ; Log output interval (timesteps)
nstenergy = 50 ; Energy output interval (timesteps)
nstcalcenergy = 50 ; Energy calculation interval (timesteps)
