[gmx-users] same simulation, different results

[David van der Spoel]

Jim Fonseca wrote:
> 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

Is this 3.2.1? The optimize_fft may make your simulations differ 
because, depending on timing, a different algorithm may be used. Change 
this flag to no and test again.


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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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