[gmx-users] checkpoint file and *.gro -- energy calculation
Yongchul Chung
yxc169 at case.edu
Sat Nov 13 18:06:10 CET 2010
Thanks Justin for your prompt reply. I am aware of the link you provided,
but it seems they are rather hand-waving. It would be nice if I could be
directed to a source code of some sort.
Greg
On Sat, Nov 13, 2010 at 11:50 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Yongchul Chung wrote:
>
>> Hello gmx-users,
>>
>> I ran two short simulation in series (simulation A --> simulation B). The
>> output *.gro file from the simulation A was used as an input file for the
>> simulation B. If I compare the energy value at the end of simulation A, and
>> t=0 at simulation B, they are different (<0.1% deviation). However, if you
>> supply checkpoint file, you get exactly the same value of the energy at t=0
>> for simulation B. I used gmxdump to check out the contents of cpt file. It
>> seems like the file has some extra components compared to gro file (which
>> has position, and velocity information). Several extra things I found that
>> might be relevant were 'energy_aver', 'energy_sum', and 'energy_n[0]'. It
>> seems like gromacs somehow use these values internally to match the energy
>> value at the start of simulation B to the end of simulation A.
>> Can someone tell me why there's an error in the energy value if we don't
>> supply the cpt file, but with cpt file, there's no error? I suspect it has
>> to do with the extra information I mentioned above, but not sure where in
>> the source code to look for more information.
>>
>
> I can't provide any information on the specifics in the code, but if you
> think about the purpose and function of the .cpt file, it makes sense. The
> .cpt file contains information about the entire state of the system, which
> is described by more than just position and velocities, which, in the .gro
> file, are in limited precision.
>
> For a bit more:
>
>
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations#Exact_vs_binary_identical_continuation
>
> -Justin
>
>
> Thanks,
>>
>> Greg
>>
>> I'm appending the data, commands, and mdp file below for the reference.
>>
>> // commands
>> 1) Simulation A
>> grompp -f grompp.mdp -c input_to_A.gro -n index.ndx -p topol.top
>> mdrun -s topol.tpr -c output_of_A.gro
>>
>> 2-1) Simulation B (w/o checkpoint)
>> grompp -f grompp.mdp -c output_of_A.gro -n index.ndx -p topol.top
>> mdrun -s topol.tpr -c output_of_B.gro
>>
>> 2-2) Simulation B(w/ checkpoint)
>> grompp -f grompp.mdp -c output of A.gro -n index.ndx -p topol.top -t
>> state.cpt
>> mdrun -s topol.tpr -c output_of_B_with_state.gro
>>
>> // data
>> Simulation A energy data
>> time bond bond-nc
>> angles dihedral LJ(SR)
>> potential kinetic total energy
>> 0.000000 29233.408203 43995.722656 45702.835938 51693.003906
>> -144114.109375 26510.859375 85977.609375 112488.468750
>> 0.003000 29246.806641 44015.367188 45684.222656 51694.019531
>> -144110.906250 26529.500000 85964.890625 112494.390625
>> 0.006000 29247.708984 44022.949219 45585.886719 51695.375000
>> -144107.500000 26444.421875 86054.156250 112498.578125
>> 0.009000 29241.958984 44016.546875 45426.968750 51697.175781
>> -144104.265625 26278.390625 86218.250000 112496.640625
>> 0.012000 29235.324219 44005.812500 45257.687500 51699.402344
>> -144101.031250 26097.203125 86396.218750 112493.421875
>> 0.015000 29231.802734 43999.378906 45130.500000 51701.945312
>> -144098.000000 25965.625000 86528.429688 112494.054688
>> 0.018000 29231.041016 43994.878906 45067.519531 51704.746094
>> -144094.390625 25903.796875 86595.398438 112499.195312
>> 0.021000 29227.580078 43988.855469 45058.753906 51707.007812
>> -144091.468750 25890.718750 86615.390625 112506.109375
>> 0.024000 29213.531250 43979.210938 45072.437500 51708.511719
>> -144088.968750 25884.718750 86626.640625 112511.359375
>> 0.027000 29182.050781 43970.894531 45074.558594 51708.472656
>> -144086.500000 25849.468750 86666.546875 112516.015625
>> 0.030000 29130.822266 43963.402344 45045.148438 51706.945312
>> -144083.968750 25762.343750 86753.906250 112516.250000
>>
>> Simulation B energy data (w/o checkpoint supply)
>> time bond bond-nc
>> angles dihedral LJ(SR)
>> potential kinetic total energy
>> 0.000000 29177.361328 43958.375000 45142.761719 51717.425781
>> -144082.890625 25913.031250 86762.046875 112675.078125
>> 0.003000 29105.240234 43942.156250 45086.699219 51714.648438
>> -144080.843750 25767.906250 86901.765625 112669.671875
>> 0.006000 29024.171875 43924.238281 45048.691406 51711.386719
>> -144079.562500 25628.921875 87035.437500 112664.359375
>> 0.009000 28946.726562 43907.777344 45057.507812 51707.562500
>> -144078.187500 25541.375000 87120.882812 112662.257812
>> 0.012000 28883.349609 43891.914062 45115.203125 51703.593750
>> -144076.875000 25517.187500 87146.593750 112663.781250
>> 0.015000 28838.960938 43876.933594 45194.253906 51698.367188
>> -144075.921875 25532.578125 87133.734375 112666.312500
>> 0.018000 28811.880859 43862.824219 45258.449219 51691.171875
>> -144074.359375 25549.968750 87119.765625 112669.734375
>> 0.021000 28797.781250 43848.613281 45278.308594 51680.550781
>> -144072.375000 25532.875000 87136.203125 112669.078125
>> 0.024000 28790.947266 43837.628906 45248.121094 51666.472656
>> -144069.750000 25473.421875 87192.453125 112665.875000
>> 0.027000 28788.593750 43833.882812 45184.238281 51649.878906
>> -144066.250000 25390.343750 87271.281250 112661.625000
>> 0.030000 28791.101562 43838.437500 45111.562500 51631.695312
>> -144062.437500 25310.359375 87347.335938 112657.695312
>>
>> Simulation B energy data (w/ checkpoint supply)
>> time bond bond-nc
>> angles dihedral LJ(SR)
>> potential kinetic total energy
>> 0.000000 29130.822266 43963.402344 45045.148438 51706.945312
>> -144083.968750 25762.343750 86753.906250 112516.250000
>> 0.003000 29062.935547 43950.101562 45003.597656 51704.625000
>> -144082.593750 25638.671875 86871.796875 112510.468750
>> 0.006000 28987.000000 43933.789062 44987.125000 51702.902344
>> -144080.546875 25530.265625 86977.445312 112507.710938
>> 0.009000 28915.218750 43915.363281 45016.925781 51700.277344
>> -144079.140625 25468.640625 87037.531250 112506.171875
>> 0.012000 28857.343750 43895.234375 45089.933594 51697.753906
>> -144077.906250 25462.359375 87046.164062 112508.523438
>> 0.015000 28817.451172 43875.136719 45177.636719 51693.886719
>> -144077.312500 25486.796875 87024.257812 112511.054688
>> 0.018000 28794.009766 43857.585938 45244.371094 51687.488281
>> -144075.656250 25507.796875 87008.031250 112515.828125
>> 0.021000 28782.230469 43840.925781 45260.535156 51677.023438
>> -144073.578125 25487.140625 87028.789062 112515.929688
>> 0.024000 28777.083984 43828.734375 45221.421875 51662.421875
>> -144071.265625 25418.390625 87094.679688 112513.070312
>> 0.027000 28775.339844 43824.812500 45144.421875 51644.714844
>> -144067.640625 25321.656250 87187.125000 112508.781250
>> 0.030000 28777.638672 43829.210938 45058.011719 51625.828125
>> -144064.296875 25226.390625 87277.976562 112504.367188
>>
>> // mdp
>>
>> ; RUN CONTROL PARAMETERS
>> integrator = md
>> ; Start time and timestep in ps
>> tinit = 0.0
>> dt = 0.003
>> ;nsteps = 10000000
>> nsteps = 10
>> ; For exact run continuation or redoing part of a run
>> init_step = 0
>> ; mode for center of mass motion removal
>> comm-mode = Linear
>> ; number of steps for center of mass motion removal
>> nstcomm = 100
>> ; group(s) for center of mass motion removal
>> comm-grps =
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout = 1
>> nstvout = 1
>> nstfout = 1
>> ; Checkpointing helps you continue after crashes
>> nstcheckpoint = 1
>> ; Output frequency for energies to log file and energy file
>> nstlog = 1
>> nstenergy = 1
>> ; Output frequency and precision for xtc file
>> nstxtcout = xtc_precision = 1000
>> ; This selects the subset of atoms for the xtc file. You can
>> ; select multiple groups. By default all atoms will be written.
>> xtc-grps =
>> ; Selection of energy groups
>> energygrps = A B
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist = 1
>> ; ns algorithm (simple or grid)
>> ns_type = grid
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>> ; or full (infinite systems only)
>> pbc = xyz
>> ; nblist cut-off
>> rlist = 1.1
>> ;domain-decomposition = no
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>> ; Temperature coupling
>> ;tcoupl = no
>> tcoupl = Berendsen
>> ;tcoupl = v-rescale
>> ; Groups to couple separately
>> tc-grps = system
>> ; Time constant (ps) and reference temperature (K)
>> tau_t = 0.5
>> ref_t = 363
>> ; Pressure coupling
>> Pcoupl = no
>> ;Pcoupl = Berendsen
>> Pcoupltype = Anisotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>> tau_p = 0.33
>> compressibility = 0 0 0 0 0 0
>> ref_p = 1.01325 1.01325 1.01325 0 0 0
>> ; Random seed for Andersen thermostat
>> andersen_seed = -1
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN
>> gen_vel = no
>> gen_temp = 363
>> gen_seed = 57597
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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