[gmx-users] OpenMM

PACIELLO GIULIA giulia.paciello at polito.it
Thu Apr 15 08:27:04 CEST 2010

The two tables was the averages generated by the serial 
code and by the parallel code (I have used, as you suggest 
me, the option rerun of mdrun on the CPU to analyze the 
energies obtained with the parallel simulation on 
GPU)...Could you tell me if these results could be correct 
and why?

I have also another question...in a precedent post you 
said me that .gro files from serial and parallel codes are 
different for two main reasons: the architecture used to 
simulate the ensamble and the algorithms implemented. 
Could you tell me more about this? If MD is deterministic 
which is the correct solution? Which are the 
approximations done?

Thanks a lot,

On Thu, 15 Apr 2010 08:53:07 +1000
  Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 14/04/2010 7:10 PM, PACIELLO GIULIA wrote:
>> Well,
>> I have used the option -rerun to 'rerun' on CPU the 
>>simulation from the
>> parallel code. As you can see in the following tables, 
>>results are very
>> similar for non bonded terms, but not for the other 
>>energetic terms
>> (these are avereges obtained from g_energy):
> You haven't done a simulation. You've done an energy 
>minimization. There's no reason to expect the same result 
>for EM on different machines because there are so many 
>different minima that might be found, and small numerical 
>differences might mean you find different ones.
>> Angle: 4256.27
>> Prop-di: 322.302
>> R-B: 3101.14
>> LJ-14: 2107.6
>> Coul-14: 15212
>> LJ(SR): -3410.22
>> Coul(SR): -29368.3
>> RF(excl): -9425.23
>> Pot.En: -17204.5
>> Kin.En: 5243.87
>> Tot.En: -11960.6
>> Angle: 6089.56
>> Prop-di: 466.121
>> R-B: 3677.95
>> LJ-14: 2234.85
>> Coul-14: 15149.8
>> LJ(SR): -3144
>> Coul(SR): -29240.7
>> RF(excl): -9425.25
>> Pot.En: -14191.7
>> Kin.En: 8262.96
>> Tot.En: -5929.78
>> I can't use the -reprod option, but I have noticed that 
>>the .gro files
>> after the energy minimization are very similar (I have 
>>performed this
>> minimization on the .gro files obtained running the 
>>parallel and serial
>> codes)...systems are converging to the same equilibrium 
> No, they've just done an EM. There's no velocities yet, 
>so they're not in any ensemble. Equilibrate, and then 
>look at ensemble averages of the equilibrated systems.
> Mark
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