[gmx-users] temperature problem

[Lovika Moudgil]

Hi everyone


I am having some problem in my md run .In my system temperature of system
is abruptly increasing .I have done nvt for 50 picoseconds ..nd then using
it for further md simulation .I am not getting any error for this
temperature increase .....But when I plot temperature graph , temperature
is not same as nvt and is very high  in md .I am having gold slab and amino
acid in my system . Mdp file for md run is below ....Is their any error in
my mdp file ???what could be the reason for this ???Please suggest ....
; Run parameters
integrator    = md        ; leap-frog integrator
nsteps        = 30000000        ; 2 * 50000 = 100 ps
dt        = 0.001        ; 2 fs
; Output control
; Output control
nstxout        = 500        ; save coordinates every 1.0 ps
nstvout        = 500        ; save velocities every 1.0 ps
nstenergy    = 500        ; save energies every 1.0 ps
nstlog        = 500        ; update log file every 1.0 ps
nstxtcout               = 500           ; [steps] freq to write coordinates
to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc
trajectory
energygrps              = System        ; group(s) to write to energy file
; Bond parameters

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
cutoff-scheme       = Verlet
ns_type            = grid        ; search neighboring grid cells
nstlist            = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.0        ; short-range electrostatic cutoff (in nm)
rvdw            = 1.0        ; short-range van der Waals cutoff (in nm)

; Electrostatics
coulombtype         = cut-off
pme_order        = 4        ; cubic interpolation
fourierspacing        = 0.12    ; grid spacing for FFT
; Temperature coupling is on
tcoupl        = nose-hoover                ; modified Berendsen thermostat
tc-grps        = Protein AUS AUB AUI SOL NA CL    ; two coupling groups -
more accurate
tau_t        = 0.1   0.1 0.1 0.1 0.1 0.1  0.1         ; time constant, in ps
ref_t        = 300     300 300 300 300 300  300        ; reference
temperature, one for each group, in K
; Pressure coupling is off
pcoupl        = no         ; no pressure coupling in NVT
; Periodic boundary conditions
pbc        = xyz            ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres    ; account for cut-off vdW scheme
; Velocity generation
; Velocity generation
gen_vel        = yes        ; assign velocities from Maxwell distribution
gen_temp    = 300        ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps               = AUS AUB AUI
freezedim                = Y Y Y Y Y Y Y Y Y
comm_mode                = None

Thanks and Reagrds
Lovika