Dear gmxusers, Thank you for your answers so far. I have run a few more test rerun and here is what I got: -The number of degree of freedom are the same whatever the topology I run with, both in the log file and from the grompp output. -Comparing the trajectories created from rerun with gmxdump and diff show only minor differences, such as atoms positioned on one side or the other of the simulation box. The velocities are strictly the same however. Here is an example:
8836288,8836290c8836288,8836290 < x[394728]={ 1.32183e+02, 3.15341e+00, 5.17869e+00} < x[394729]={ 1.32054e+02, 3.10839e+00, 5.14599e+00} < x[394730]={ 1.32314e+02, 3.17612e+00, 5.13366e+00} --- > x[394728]={-7.17163e-04, 3.15341e+00, 5.17869e+00} > x[394729]={-1.29196e-01, 3.10839e+00, 5.14599e+00} > x[394730]={ 1.29883e-01, 3.17612e+00, 5.13366e+00} -If I use another topology where I only have the interaction with water not set to zero (still with electrostatic), I get a temperature of ~326K intermediate between the desired value of 325K and the value I got with all the interaction shutdown of ~327K. -Turning the temperature/pressure coupling on or off do not change the results. I think there is a problem in the calculation of the kinetic energy that translate to the temperature. However setting all the interaction but the electrostatic to zero should not modify the kinetic energy calculated from 'mdrun -rerun'. I do not know how to proceed from here, maybe I should post my mdp top and log files here or on the developers forum ? Have a good day, Bastien Loubet -- View this message in context: http://gromacs.5086.n6.nabble.com/Possible-bug-in-the-temperature-calculation-from-rerun-tp5001194p5001508.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