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On 19/11/2011 10:10 PM, Igor Druz wrote:
<blockquote
cite="mid:CAPEHq6_AHULjOUO8o4=3S8Ljr93q5wAF-9OeUM6a+BJcd-woNg@mail.gmail.com"
type="cite">Hello,
<div><br>
</div>
<div>I am running MDs on a linux PC with OpenSuse, using:</div>
<div><br>
</div>
<div>mpirun -np 4 mdrun -v -dlb auto -reprod ....</div>
<div><br>
</div>
<div>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.</div>
</blockquote>
<br>
Yep. <a
href="http://www.gromacs.org/Documentation/Terminology/Reproducibility">http://www.gromacs.org/Documentation/Terminology/Reproducibility</a><br>
<br>
<blockquote
cite="mid:CAPEHq6_AHULjOUO8o4=3S8Ljr93q5wAF-9OeUM6a+BJcd-woNg@mail.gmail.com"
type="cite">
<div> 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: <br>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPEHq6_AHULjOUO8o4=3S8Ljr93q5wAF-9OeUM6a+BJcd-woNg@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>
<div>cpp = /usr/bin/cpp -traditional</div>
<div>integrator = sd</div>
<div>tinit = 0</div>
<div>dt = 0.002</div>
<div>nsteps = 1000000</div>
<div><br>
</div>
<div>nstcomm = 1</div>
<div>nstcalcenergy = 1</div>
<div>nstxout = 5</div>
<div>nstvout = 100</div>
<div>nstlog = 100</div>
<div>nstenergy = 100</div>
<div><br>
</div>
<div>nstlist = 5</div>
<div>ns_type = grid</div>
<div><br>
</div>
<div>pbc = xyz</div>
<div>rlist = 0.9</div>
<div><br>
</div>
<div>optimize_fft = yes</div>
<div>coulombtype = pme</div>
<div>rcoulomb = 0.9</div>
<div>epsilon-r = 1</div>
<div>rvdw = 0.9</div>
</div>
<div><br>
</div>
<div>
<div>constraints = all-bonds</div>
<div>constraint-algorithm = Lincs</div>
<div><br>
</div>
<div>unconstrained-start = yes</div>
<div>lincs-warnangle = 30</div>
</div>
<div>
<div><br>
</div>
<div>tc_grps = System</div>
<div>tau_t = 0.1</div>
<div>ref_t = 300.0</div>
<div><br>
</div>
<div>Pcoupl = parrinello-rahman</div>
<div>tau_p = 2</div>
<div>compressibility = 4.5e-05</div>
<div>ref_p = 1.0</div>
<div><br>
</div>
<div>gen_vel = yes</div>
<div>gen_temp = 300.0</div>
<div>gen_seed = 173529</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div>Many thanks for your help,</div>
<div>
Igor</div>
<br>
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<br>
</blockquote>
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