[gmx-users] problems with randoms seeds

[Thomas Schlesier]

hi all,
i'm trying out GROMACS 4.5.3
i'm simulating (sd-integrator) a small rna hairpin in vacuum, without 
pbc for 100ps. System has about 380 atoms.
If i do the simulation a second time (grompp + mdrun) i get identical 
results.
first i had only *gen_seed = -1* but latter i set also *ld_seed = -1*, 
but nothing changes.

one thing which really confuses me is the ld_seed:
output from grompp:
Setting the LD random seed to 1870
md.log:
ld_seed              = 1993

position restraints are only applied to 3atoms.

has anyone an idea what happens?

greetings
thomas


here is the mdp-file:
OPLS Lysozyme NVT equilibration
define          = -DPOSRES      ; position restrain the protein
; Run parameters
integrator      = sd            ; leap-frog integrator
nsteps          = 50000         ; 2 * 50000 = 100 ps
dt              = 0.002         ; 2 fs
comm_mode       = angular
; 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    = no            ; 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         = simple        ; search neighboring grid cells
nstlist         = 0             ; 10 fs
rlist           = 0.0           ; short-range neighborlist cutoff (in nm)
rcoulomb        = 0.0           ; short-range electrostatic cutoff (in nm)
rvdw            = 0.0           ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = cut-off       ; Particle Mesh Ewald for long-range 
electrostatics
; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = System        ; two coupling groups - more accurate
tau_t           = 2.0           ; time constant, in ps
ref_t           = 300           ; reference temperature, one for each 
group, in K
; Pressure coupling is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = no            ; 3-D PBC
; Velocity generation
gen_vel         = yes           ; assign velocities from Maxwell 
distribution
gen_temp        = 300           ; temperature for Maxwell distribution
gen_seed        = -1            ; generate a random seed
ld_seed         = -1