Forgot to mention that I am using gromacs 4.0.3 with N=19200 Greg
On Sat, Nov 13, 2010 at 12:06 PM, Yongchul Chung <yxc...@case.edu> 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. > > 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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