[gmx-users] checkpoint file and *.gro -- energy calculation
Yongchul Chung
yxc169 at case.edu
Sat Nov 13 18:42:49 CET 2010
Thanks, Mark.
Greg
On Sat, Nov 13, 2010 at 12:35 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 14/11/2010 4:06 AM, Yongchul Chung wrote:
>
> 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.
>
>
> They're "hand-waving" by design of course - a normal user doesn't care
> about the details so long as they know how to make it work right.
>
> src/gmxlib/checkpoint.c has the details (in 4.5 at least), which vary quite
> a bit with MD algorithm and GROMACS version.
>
> Mark
>
>
>
> 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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>
>
>
> --
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