[gmx-users] Reproducable MD runs on two PCs

[Mark Abraham]

On 19/11/2011 10:10 PM, Igor Druz wrote:
> Hello,
>
> I am running MDs on a linux PC with OpenSuse, using:
>
> mpirun -np 4 mdrun -v -dlb auto -reprod ....
>
> If I repeat the calculation on the same PC, I get the same result. If 
> I change to another PC with RedHat I get a different result.

Yep. http://www.gromacs.org/Documentation/Terminology/Reproducibility

> More specifically, I am calculating a deviation from experiment, which 
> varies by ~20 % on changing operating systems (pretty much the same 
> hardware on both PCs). Is there any way to avoid such variations? I 
> guess I am missing something in the mdp file, which is:

Change your gen_vel seed and I bet you observe a similar variation on 
the same machine. There are rather few systems that will have 
equilibrated in 2ns, never mind converged.

Mark

>
> cpp                 =  /usr/bin/cpp -traditional
> integrator               = sd
> tinit                    = 0
> dt                       = 0.002
> nsteps                   = 1000000
>
> nstcomm                  = 1
> nstcalcenergy            = 1
> nstxout                  = 5
> nstvout                  = 100
> nstlog                   = 100
> nstenergy                = 100
>
> nstlist                  =  5
> ns_type                  = grid
>
> pbc                      = xyz
> rlist                    = 0.9
>
> optimize_fft             = yes
> coulombtype              = pme
> rcoulomb                 = 0.9
> epsilon-r                = 1
> rvdw                     = 0.9
>
> constraints              = all-bonds
> constraint-algorithm     = Lincs
>
> unconstrained-start      = yes
> lincs-warnangle          = 30
>
> tc_grps                  = System
> tau_t                    = 0.1
> ref_t                    = 300.0
>
> Pcoupl                   = parrinello-rahman
> tau_p                    = 2
> compressibility         = 4.5e-05
> ref_p                    = 1.0
>
> gen_vel                  = yes
> gen_temp                 = 300.0
> gen_seed                 = 173529
>
>
> Many thanks for your help,
> Igor
>
>

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