[gmx-users] same simulation, different results

[Jim Fonseca]

Hi,
Does anyone know what would cause a simulation to change if I run it  
a second time?  I'm starting with an EM structure and just doing a  
quick 10 ps simulation.  I've found that (in one case) the energies  
start to differ somewhere between step 200 and step 250--the Vir and  
Pres values differ first.  I can't figure out what else besides  
gen_vel and gen_seed would give me different results.  I'm running on  
the same system, same number of processors, etc. I'm pasting my .mdp  
below.  I realize I'm probably overlooking something, but can anyone  
help me with this?

Thank you,
Jim Fonseca

title                    = PG_Ca_ext
cpp                      = /usr/bin/cpp
include                  = -I../top
constraints		 = all-bonds
integrator               = md
tinit                    = 0.0
dt                       = 0.002
nsteps                   = 10000   ;20 ps
nstxout                  = 10000
nstvout                  = 10000
nstlog                   = 10000
nstenergy                = 50
nstxtcout                = 50
xtc_grps                 = Protein  SOL_Na_Ca POP
energygrps               = Protein  SOL_Na_Ca POP
nstlist                  = 10
ns_type                  = grid
rlist                    = 1.4
coulombtype              = PME
rcoulomb                 = 1.4
rvdw                     = 1.4
tcoupl                   = Berendsen
tc-grps                  = Protein      SOL_Na_Ca    POP
tau_t                    = 0.1  0.1  0.1
ref_t                    = 300  300  300
Pcoupl                   = Berendsen
pcoupltype		 = anisotropic
tau_p                    = 1.0
compressibility          = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
ref_p                    = 1.5 1.5 1.5 0.0 0.0 0.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 161803
optimize_fft		 = yes