[gmx-users] OpenMM

PACIELLO GIULIA giulia.paciello at polito.it
Wed Apr 14 11:10:57 CEST 2010

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):

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 

I'm thankful for your help,

On Wed, 14 Apr 2010 18:03:43 +1000
  Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 14/04/2010 5:18 PM, PACIELLO GIULIA wrote:
>> I dont'know if this is the right way to test that things 
>>converge to the
>> same value...but I have made an energy minimization on 
>>CPU of the two
>> output (parallel and serial). I have obtained this 
>> Potential Energy = -1.6960029e+04
>> Maximum force = 1.7282695e+03 on atom 364
>> Norm of force = 4.6171844e+02
>> Potential Energy = -1.7814945e+04
>> Maximum force = 2.1551072e+03 on atom 496
>> Norm of force = 2.9537823e+02
> They're probably both fine. By "converged" I was 
>referring to an equilibrium MD ensemble.
> Mark
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