[gmx-users] Possible bug with -rerun option

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 19 20:46:12 CEST 2006


Alexandre Suman de Araujo wrote:
> Hi GMXers
> 
> I observed a strange behavior in a simulation of an equilibrated box
> with 1409 tip3p water molecules using OPLS-AA, PME and GROMACS 3.3.1 in
> double precision.
> My .mdp file is as fallow:
> 
the problem is in the averaging. since you save coordinates every 
hundred steps averaging gives a factor 100 difference. Note that the 
average value in a rerun will never be the same as in the original run 
since you are missing 99/100 frames. The instantaneous energies should 
be the same however.

Please submit a bugzilla about averaging in mdrun -rerun and edr files 
resulting from such runs.

> ;
> ;       Input file
> ;
> title               =  Simulacao de calculo   
> cpp                 =  /lib/cpp               
> dt                  =  0.001                 
> integrator          =  md                    
> nsteps              =  10000                  
> nstcomm             =  1                       
> nstxout             =  100                     
> nstvout             =  100                    
> nstlog              =  100                    
> nstenergy           =  100                 
> nstlist             =  10                      
> ns_type             =  grid                  
> pbc                 =  xyz                   
> rlist               =  0.9               
> coulombtype         =  PME                   
> rcoulomb            =  0.9                   
> vdwtype             =  cut-off             
> rvdw                =  0.9                   
> tcoupl              =  berendsen        
> ref_t               =  300                  
> tc-grps             =  System               
> tau_t               =  0.1                   
> pcoupl              =  berendsen            
> pcoupltype          =  isotropic             
> tau_p               =  1                    
> compressibility     =  4.5e-5
> ref_p               =  1.0
> 
> Finishing the simulation I run g_energy in the .edr, obtaining the
> follow results:
> 
> Statistics over 10001 steps [ 0.0000 thru 10.0000 ps ], 3 data sets
> 
> Energy                      Average       RMSD     Fluct.      Drift 
> Tot-Drift
> -------------------------------------------------------------------------------
> Potential                  *-55852.6*    136.692        136  
> -4.75933    -47.598
> Total-Energy               *-45314.7*    78.2564    77.8627   -2.71554  
> -27.1581
> Temperature                 *299.942*    3.15335    3.14887   0.058173  
> 0.581788
> Heat Capacity Cv:      12.4738 J/mol K (factor = 0.000110527)
> 
> Until here everything is ok. So I used the same .tpr file and -rerun
> option in mdrun_d in the trajectory from this first simulation. So I ran
> g_energy in the new .edr file and obtained:
> 
> Statistics over 10001 steps [ 0.0000 thru 10.0000 ps ], 3 data sets
> 
> Energy                      Average       RMSD     Fluct.      Drift 
> Tot-Drift
> -------------------------------------------------------------------------------
> Potential                  *-563.871*    5526.06    5526.05  
> -4.75933    -47.598
> Total-Energy               *-457.605*    4484.56    4484.55   
> -2.9575    -29.578
> Temperature                 *3.02467*    29.6455    29.6451  0.0512859  
> 0.512911
> Heat Capacity Cv:   -0.0871562 J/mol K (factor = 96.0644)
> 
> It can be seen that there are differences of approximately a factor 100
> between Average values.
> 
> 
> In the .log files I saw the follow results:
> 
> First Simulation:
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.90375e+03   -5.73880e+04   -7.13930e+03   *-5.56236e+04 *  
> 1.04571e+04
>    Total Energy    Temperature Pressure (bar)
>    *-4.51665e+04*    *2.97643e+02*    4.12898e+02
> 
>            Step           Time         Lambda
>           10000       10.00000        0.00000
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.36435e+03   -5.68959e+04   -7.10656e+03   *-5.56381e+04*   
> 1.05288e+04
>    Total Energy    Temperature Pressure (bar)
>    *-4.51094e+04*    *2.99683e+02*   -2.69511e+02
> 
>         <======  ###############  ==>
>         <====  A V E R A G E S  ====>
>         <==  ###############  ======>
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.68022e+03   -5.74019e+04   -7.13085e+03   *-5.58526e+04*   
> 1.05378e+04
>    Total Energy    Temperature Pressure (bar)
>    *-4.53147e+04*    *2.99942e+02*    1.07997e+01
> 
> 
> 
> 
> 
> Second Simulation (rerun):
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.90375e+03   -5.73880e+04   -7.13930e+03   *-5.56236e+04*   
> 1.04594e+04
>    Total Energy    Temperature Pressure (bar)
>    *-4.51641e+04*    *2.97709e+02*    4.13037e+02
> 
>            Step           Time         Lambda
>           10000       10.00000        0.00000
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.36435e+03   -5.68959e+04   -7.10656e+03   *-5.56381e+04*   
> 1.05293e+04
>    Total Energy    Temperature Pressure (bar)
>    *-4.51088e+04*    *2.99699e+02*   -2.70138e+02
> 
>         <======  ###############  ==>
>         <====  A V E R A G E S  ====>
>         <==  ###############  ======>
> 
>    Energies (kJ/mol)
>         LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>     8.79288e+01   -5.79793e+02   -7.20063e+01   *-5.63871e+02*   
> 1.06266e+02
>    Total Energy    Temperature Pressure (bar)
>    *-4.57605e+02*    *3.02467e+00*    4.68805e-01
> 
> Here we observed again that in the first simulation everything is ok,
> but in the "reran" simulation the Average values are approximately 100
> times lesser than the values obtained in every step (the values are in
> bold)!!!
> I made this test with GROMACS 2.2.1 in single precision and this
> behavior happened too.
> 
> This could be a bug??? Or am I doing something wrong????
> 
> Best regards.
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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