[gmx-users] NPT equilibration

[shivangi nangia]

Hello,

I am having problems in carrying out a NPT equilibration of my system at 500
K.

System: A 5 nm cube with peptide, Li+ ions and 2,5-dihydroxybenzoic acid
anion.

NVT equilibration gives expected results.

When I load the npt.gro file in VMD, its seems as if the molecules have
fragmented/vaporized.

nvt.mdp:

title    = hist 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     = 100    ; save coordinates every 0.2 ps
nstvout     = 100    ; save velocities every 0.2 ps
nstenergy   = 100    ; save energies every 0.2 ps
nstlog      = 100    ; update log file every 0.2 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     = 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 is on
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    = 500    500   ; 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
; Periodic boundary conditions
pbc      = xyz    ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no     ; Velocity generation is off


If I use the same exact system and run NVT and NPT equilibration at 300 K,
everything seems to be working.

What could be going wrong at 500 K?

Thanks,
Shivangi
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