[gmx-users] Equilibrating Water around the Molecule

[Lara Bunte]

Hello

I want to equilibrate the water around my molecule. For doing this I created a pr.mdp file that makes most sense for me. Sadly I am a beginner with less knowledge, so could you please take a look on this pr.mdp file and say me if this is good or if not, what would you suggest to me? My System is Isoalloxazin in a water box. I use a CHARMM27 force field and a tip3p water model. Here is the file:

title           = isoalloxazin NPT equilibration
define      = -DPOSRES  ; position restrain the protein

; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000         ; 2 * 50000 = 100 ps
dt              = 0.002         ; 2 fs

; Output control
nstxout         = 5000          ; save coordinates every 4 ps
nstvout         = 5000          ; save velocities every 4 ps
nstenergy       = 5000          ; save energies every 4 ps
nstlog          = 5000          ; update log file every 4 ps

; Bond parameters
continuation    = yes           ; Restarting after NVT
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds) constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy

; Neighborsearching
ns_type         = grid          ; search neighboring grid cells
nstlist         = 1             ; edited to 1
rlist           = 1.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0           ; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range electrostatics
pme_order       = 4             ; cubic interpolation
fourierspacing  = 0.12          ; grid spacing for FFT

; Temperature coupling is on
tcoupl           = nose-hoover
tc-grps         = Isoalloxazin Sol   
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 300   300     ; reference temperature, one for each group, in K

; Pressure coupling is on
pcoupl          = Parrinello-Rahman     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water, bar^-1

; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

Thanks for helping me
Greetings
Lara