[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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