[gmx-users] strange jumping in the frames
I am running Metadynamics with gromacs, I saw a jump in the frame after the simulation was running for a while, I copy here part of the log file: Step Time Lambda 2055750041115.00.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.54705e+032.44201e+031.44990e+031.94769e+042.63535e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.09459e+05 -5.86065e+04 -2.14796e+055.09371e+04 -1.63859e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.66948e+053.47266e+02 -2.03134e+022.74833e-05 DD step 2055 vol min/aver 0.846 load imb.: force 0.4% Step Time Lambda 205641120.00.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.36185e+032.48355e+031.45350e+031.94714e+042.67211e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.09297e+05 -5.86137e+04 -2.14420e+055.18801e+04 -1.62540e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.67082e+053.53695e+027.73024e+012.66928e-05 DD step 20562499 vol min/aver 0.825 load imb.: force 0.6% Step Time Lambda 2056250041125.003910.0 Energies (kJ/mol) AngleProper Dih. LJ-14 Coulomb-14LJ (SR) 3.55493e+032.49077e+031.45219e+031.93942e+042.60391e+04 Coulomb (SR) Coul. recip. PotentialKinetic En. Total Energy -2.08596e+05 -5.86454e+04 -2.14310e+055.14416e+04 -1.62868e+05 Conserved En.Temperature Pressure (bar) Cons. rmsd () -1.67250e+053.50706e+02 -3.50552e+022.93757e-05 as you can see the time jumped from 41120.0 to 41125.00391 , while it has to be 41125.0 and then it continue the rest of simulation like this, Do you what is the problem ?!! Fahimeh -- gmx-users mailing listgmx-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
Re: [gmx-users] strange jumping in the frames
as you can see the time jumped from 41120.0 to 41125.00391 , while it has to be 41125.0 and then it continue the rest of simulation like this, Do you what is the problem ?!! Probably no problem at all. Numbers that are readily represented in decimal notation, like a timestep of 0.002ps, need not have an exact representation in *binary* floating point. If they don't, then when you add up a large number of them, then you can accumulate rounding error. Probably, if you run grep 0\.0 *.log then you will see other times reported that have not rounded nicely. My best guess is that your simulation stopped at this point, and restarted from the step corresponding to 41125.004ps, and rounding error is doing the rest. Mark -- gmx-users mailing listgmx-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
