Dear gmx users, We recently got a problem with the rerun feature of mdrun, and we request your help in order to help to solve it.
We have run a simulation of a large POPC membrane using the coarse grained Martini force fields. From these simulations we obtained a trr trajectory file which contains both the position and the velocity of each martini particle every 20 ps. From this trajectory we rerun the simulation using the -rerun option of the mdrun program but with a different topology for which we have set all the bonded and non bonded interaction to zero. Specifically we have set all the force constant to zero in the martini_v2.P.itp and the martini_v2.0_lipids.itp file, the aim is to calculate the virial due to the electrostatic forces alone. The problem is the following: from the edr file we get from the rerun we extract the mean value of the energies using g_energy. For the edr file obtained during the simulation (and not the rerun) we obtained for the temperature and the kinetic energy, using also a 20ps time interval: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 324.998 0.0049 0.413669 -0.00743801 (K) Kinetic En. 1.9525e+06 29 2485.21 -44.6815 (kJ/mol) This is to be expected because we have a Nose-Hover temperature coupling of 325 K. The kinetic energy is also equals to the number of degree of freedom times half the Boltzmann constant times the temperature. However for the rerun, with no bonded and non-bonded interactions, we get: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 327.35 0.0053 0.415978 -0.00514402 (K) Kinetic En. 1.96663e+06 32 2499.08 -30.8973 (kJ/mol) The kinetic energy is again equals to the number of degree of freedom times half the Boltzmann constant times the temperature, however the temperature is 2 K off ! This is surprising as only the velocities and the masses of the particle should enter the kinetic energy. The velocities are taken from the trr trajectory file and we have checked using the Linux diff utility that our topology have the same masses than the original one. Another cause can be that we are doing the rerun on a local machine while the original simulation was run on a cluster, however we believe that this kind of numerical error cannot be responsible for a 2 degree Kelvin mistake. Furthermore we have rerun the simulation using the original topology and we obtained: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 324.998 0.005 0.411827 -0.00761929 (K) Kinetic En. 1.9525e+06 30 2474.15 -45.7788 (kJ/mol) The slightly different value are certainly due to the previously mentioned fact that the reruns were not run on the same machine as the simulation and numerical rounding errors. This point out that it is really the topology that changes the value of the temperature. However we really have no masses differences between the two topologies and the velocities are draw from the same trr trajectory file. Any thought on this problem would be welcome. Cheers, Bastien Loubet -- View this message in context: http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun-tp5001194.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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