[gmx-users] checkpoint file and *.gro -- energy calculation
Mark Abraham
Mark.Abraham at anu.edu.au
Sat Nov 13 18:35:26 CET 2010
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
> <mailto: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 <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
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