[gmx-users] NVT equilibration

[kiana moghaddam]

Dear GMX Users

I want to equilibrate my system in NVT from 0 to 300 K then in NPT (300K). Is my mdp file in NVT equilibration is correct?

define                   = -DPOSRES 
; Run control

integrator               = md       
dt                       = 0.002 ; ps !
nsteps                   = 50000 ; total 100.0 ps.

; Output control

nstxout                  = 500 ; collect data every 1.0 ps
nstvout                  = 500 ; collect data every 1.0 ps
nstfout                  = 0
nstlog                   = 500 ; collect data every 1.0 ps
nstenergy                = 500 ; collect data every 1.0 ps
nstxtcout                = 500
xtc-precision            = 500
nstcalcenergy            = 10
energygrps               = DNA_LIG Water_counterions

; Neighbor searching and short-range nonbonded interactions
nstlist                  = 5
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0

; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.0

; van der Waals
vdw-type                 = cut-off            
rvdw                     = 1.0

; Spacing for the PME/PPPM FFT grid
fourierspacing            = 0.12

; EWALD/PME/PPPM parameters
pme_order                 = 4

; Temperature coupling
tcoupl                   = V-rescale
tc_grps                  = DNA_LIG Water_counterions
tau_t                    = 0.1     0.1 
ref_t                    = 300     300       

; SIMULATED ANNEALING  
annealing                = single single
annealing_npoints        = 7 7
annealing_time           = 0 15  30  45  60  80 100 0 15  30  45  60  80 100
annealing_temp           = 0 50 100 150 200 250 300 0 50 100 150 200 250 300

; Pressure coupling is on for NPT
pcoupl                    = no

; Dispersion correction
DispCorr                 = EnerPres
    
; generate velocities
gen_vel                   = yes  
gen_temp                  = 300
gen_seed                  = -1
 
; options for bonds
continuation             = no
constraints              = all-bonds 
constraint-algorithm     = lincs

; Highest order in the expansion of the constraint coupling matrix
lincs-order                = 4
lincs_iter                 = 1