[gmx-users] same simulation, different results

[Jim Fonseca]

Shutting off the fft optimization produced the same results for  
3.2.1.  Then I tried running two simulations using version 3.3.1 with  
the optimized fft and they differed.  Your response seemed to imply  
that the newer version should produce identical results.  Could you  
clear this up for me?

Thank you,
Jim Fonseca
On May 16, 2007, at 9:40 AM, Jim Fonseca wrote:

> 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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