You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
36 lines
1.8 KiB
36 lines
1.8 KiB
2 years ago
|
|
||
|
|
define = -DFLEXIBLE
|
||
|
|
integrator = md ; leap-frog integrator
|
||
|
|
nsteps = 100000 ; 1 * 500000 = 50 ps
|
||
|
|
dt = 0.001 ; 0.5 fs
|
||
|
|
nstxout = 100 ; save coordinates every 1.0 ps
|
||
|
|
nstenergy = 100 ; save energies every 1.0 ps
|
||
|
|
nstlog = 100 ; update log file every 1.0 ps
|
||
|
|
|
||
|
|
; Bond parameters
|
||
|
|
continuation = no ; first dynamics run
|
||
|
|
constraint_algorithm = lincs ; holonomic constraints
|
||
|
|
constraints = h-bonds ; bonds involving H are constrained
|
||
|
|
lincs_iter = 1 ; accuracy of LINCS
|
||
|
|
lincs_order = 4 ; also related to accuracy
|
||
|
|
; Nonbonded settings
|
||
|
|
cutoff-scheme = Verlet ; Buffered neighbor searching
|
||
|
|
ns_type = grid ; search neighboring grid cells
|
||
|
|
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
|
||
|
|
rcoulomb = 0.7113990804113833 ; short-range electrostatic cutoff (in nm)
|
||
|
|
rvdw = 0.7113990804113833 ; short-range van der Waals cutoff (in nm)
|
||
|
|
DispCorr = EnerPres ; account for cut-off vdW scheme
|
||
|
|
; Electrostatics
|
||
|
|
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
|
||
|
|
pme_order = 4 ; cubic interpolation
|
||
|
|
fourierspacing = 0.16 ; grid spacing for FFT
|
||
|
|
; Temperature coupling is off
|
||
|
|
tcoupl = no ; no temperature coupling in NVE
|
||
|
|
; Pressure coupling is off
|
||
|
|
pcoupl = no ; no pressure coupling in NVE
|
||
|
|
; Periodic boundary conditions
|
||
|
|
pbc = xyz ; 3-D PBC
|
||
|
|
; Velocity generation
|
||
|
|
gen_vel = no ; Velocity generation is off
|
||
|
|
|