[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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