Dear GMX users, I have some strange behaviour which I cannot explain.
I want to accelerate atoms through my box at a certain velocity. Since I can only adjust the acceleration, I have to trial-and-error my way to the right accelerations. To do this, I create a smaller 'testing' simulation, which is continued from an extensive equilibrium. I apply an acceleration of 0.05 nm/ps2, and after 200ps my velocity (gathered from gmx traj with an gmx select input) says that the velocity is stable at around 0.04 nm/ps. throughout the simulation the velocity slightly increases due to the atoms rearranging etc. Now I want to simulate the same behaviour, but for a longer amount of time. I therefore take the exact same MDP file, and change nothing except the time-related parameters. I change the number of total steps and the timestep, but leave the acceleration intact. After analysing the data I get a MUCH higher velocity! I can understand this due to rearranging of the atoms on the longer term, but after the same 200ps the velocity is also way higher. So during my smaller run the velocity was 0.04 nm/ps after 200 ps, in this longer run, the velocity is 0.2 nm/ps after the same 200ps. How is this possible? The exact same acceleration is applied. Am I missing something? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.