[gmx-users] the water box become much larger in high temporature replicas after replica exchange simulation

[#ZHANG HAIPING#]

Dear gromacs user：

I have used follow .mdp to run the replica exchange simulation, after the simulation, I find the water box become much larger in high temporature replicas, can anyone tell me how to solve this? By the way, is it caused by the water box not large enough?



title       =  replica exchange MD simulation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 500000    ;
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 0         ; suppress .trr output
nstvout     = 0         ; suppress .trr output
nstenergy   = 1000      ; save energies every 2 ps
nstlog      = 1000      ; update log file every 2 ps
nstxtcout   = 3000      ; write .xtc trajectory every 2 ps
energygrps  = Protein
; Bond parameters
continuation    = yes           ; first dynamics run
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     = 5         ; 10 fs
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  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein Non-Protein    ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 587.72   587.72                     ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for 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
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution





best regards,

Haiping