[gmx-users] OpenMM

[PACIELLO GIULIA]

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):

PARALLEL CODE
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

SERIAL CODE:
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 
ensamble?

I'm thankful for your help,
Giulia

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 
>>results:
>>
>> FROM PARALLEL OUTPUT
>> Potential Energy = -1.6960029e+04
>> Maximum force = 1.7282695e+03 on atom 364
>> Norm of force = 4.6171844e+02
>>
>> FROM SERIAL OUTPUT
>> 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
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
>http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. 
>Use the www interface or send it to 
>gmx-users-request at gromacs.org.
> Can't post? Read 
>http://www.gromacs.org/mailing_lists/users.php