Re: [gmx-users] Possible bug with -rerun option
Thanks David. The instantaneous energies are ok. I'll try to submit this to bugzilla. Best regards Alexandre Suman de Araujo [EMAIL PROTECTED] 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 = mdnsteps = >> 1 nstcomm = 1 >> nstxout = 100 nstvout = >> 100nstlog = 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 = berendsenref_t = >> 300 tc-grps = System >> tau_t = 0.1 pcoupl = >> berendsenpcoupltype = isotropic >> tau_p = 1compressibility = >> 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. thru 10. ps ], 3 data sets >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> --- >> >> Potential *-55852.6*136.692136 >> -4.75933-47.598 >> Total-Energy *-45314.7*78.256477.8627 >> -2.71554 -27.1581 >> Temperature *299.942*3.153353.14887 >> 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. thru 10. ps ], 3 data sets >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> --- >> >> Potential *-563.871*5526.065526.05 >> -4.75933-47.598 >> Total-Energy *-457.605*4484.564484.55 >> -2.9575-29.578 >> Temperature *3.02467*29.645529.6451 >> 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 EnergyTemperature Pressure (bar) >>*-4.51665e+04**2.97643e+02*4.12898e+02 >> >>Step Time Lambda >> 1 10.00.0 >> >>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 EnergyTemperature 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 EnergyTemperature Pressure (bar) >>*-4.53147e+04**2.99942e+02*1.07997e+01 >> >> >> >> >> >> Second Simulation (rerun): >> >>Energies (kJ/mol) >> LJ (SR) Coulomb (SR) Coul. recip.
Re: [gmx-users] Possible bug with -rerun option
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 = 1 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. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-55852.6*136.692136 -4.75933-47.598 Total-Energy *-45314.7*78.256477.8627 -2.71554 -27.1581 Temperature *299.942*3.153353.14887 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. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-563.871*5526.065526.05 -4.75933-47.598 Total-Energy *-457.605*4484.564484.55 -2.9575-29.578 Temperature *3.02467*29.645529.6451 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. PotentialKinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04 * 1.04571e+04 Total EnergyTemperature Pressure (bar) *-4.51665e+04**2.97643e+02*4.12898e+02 Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.36435e+03 -5.68959e+04 -7.10656e+03 *-5.56381e+04* 1.05288e+04 Total EnergyTemperature 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. PotentialKinetic En. 8.68022e+03 -5.74019e+04 -7.13085e+03 *-5.58526e+04* 1.05378e+04 Total EnergyTemperature Pressure (bar) *-4.53147e+04**2.99942e+02*1.07997e+01 Second Simulation (rerun): Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04* 1.04594e+04 Total EnergyTemperature Pressure (bar) *-4.51641e+04**2.97709e+02*4.13037e+02 Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.36435e+03 -5.68959e+04 -7.10656e+03 *-5.56381e+04* 1.05293e+04 Total EnergyTemper
[gmx-users] Possible bug with -rerun option
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: ; ; Input file ; title = Simulacao de calculo cpp = /lib/cpp dt = 0.001 integrator = md nsteps = 1 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. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-55852.6*136.692136 -4.75933-47.598 Total-Energy *-45314.7*78.256477.8627 -2.71554 -27.1581 Temperature *299.942*3.153353.14887 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. thru 10. ps ], 3 data sets Energy Average RMSD Fluct. Drift Tot-Drift --- Potential *-563.871*5526.065526.05 -4.75933-47.598 Total-Energy *-457.605*4484.564484.55 -2.9575-29.578 Temperature *3.02467*29.645529.6451 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. PotentialKinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04 * 1.04571e+04 Total EnergyTemperature Pressure (bar) *-4.51665e+04**2.97643e+02*4.12898e+02 Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.36435e+03 -5.68959e+04 -7.10656e+03 *-5.56381e+04* 1.05288e+04 Total EnergyTemperature 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. PotentialKinetic En. 8.68022e+03 -5.74019e+04 -7.13085e+03 *-5.58526e+04* 1.05378e+04 Total EnergyTemperature Pressure (bar) *-4.53147e+04**2.99942e+02*1.07997e+01 Second Simulation (rerun): Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.90375e+03 -5.73880e+04 -7.13930e+03 *-5.56236e+04* 1.04594e+04 Total EnergyTemperature Pressure (bar) *-4.51641e+04**2.97709e+02*4.13037e+02 Step Time Lambda 1 10.00.0 Energies (kJ/mol) LJ (SR) Coulomb (SR) Coul. recip. PotentialKinetic En. 8.36435e+03 -5.68959e+04 -7.10656e+03 *-5.56381e+04* 1.05293e+04 Total EnergyTemperature 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. PotentialKinetic En. 8.79288e+01 -5.79793e+02 -7.20063e+01 *-5.63871e+02* 1.06266e+02 Total EnergyTemperature Pressure (bar) *-4.57605e+02**3.02467e+00*4.68
