[gmx-users] doubt in mdrun

Shine A shine.a at iisertvm.ac.in
Wed May 1 07:29:54 CEST 2013


Sir,

        I studying the dynamics of a peptide in explicit solvent model.But
during the mdrun I got the message like this.
NOTE 1 [file md.mdp]:
  This run will generate roughly 1177130 Mb of data
why the run generating this much amount of data?
The md.mdp file I used is shown below


title           = OPLS Lysozyme MD
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 500000000     ; 2 * 500000000 = 1000000 ps, 1000 ns
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 1000          ; save coordinates every 2 ps
nstvout         = 1000          ; save velocities every 2 ps
nstxtcout       = 1000          ; xtc compressed trajectory output every 2
ps
nstenergy       = 1000          ; save energies every 2 ps
nstlog          = 1000          ; update log file every 2 ps
; Bond parameters
continuation    = yes           ; Restarting after NPT
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           = 320   320     ; 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



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