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 <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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