[gmx-users] Re: problems with randoms seeds

[Thomas Schlesier]

ok, problem solved...
used same .tpr file all the time
should stop working for today :)
greetings
thomas

On 02/22/2011 08:49 PM, Thomas Schlesier wrote:
> 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