[gmx-users] Possible bug with -rerun option
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
Thu Oct 19 18:14:28 CEST 2006
Thanks David.
The instantaneous energies are ok. I'll try to submit this to bugzilla.
Best regards
Alexandre Suman de Araujo
asaraujo at if.sc.usp.br
UIN: 6194055
IFSC - USP - São Carlos - Brasil
David van der Spoel wrote:
> 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.
>>
>
>
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