[gmx-users] same simulation, different results

[Jim Fonseca]

Thanks a lot--that was it.

On May 15, 2007, at 12:42 PM, David van der Spoel wrote:

> 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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