S. Alireza B wrote > My concern is that at the end of my 0.5 ns NVT run the T is ~300K; > however, > at the first step of my NVE, when no forces has exerted on unfrozen > molecules yet, the T appears to be ~185K!
Your explanation of this issue given in the first post sounds very meaningful. From general sense it is reasonable to consider the frozen particles just as sources of external potential field acting on the rest of the particles. So, one should not take into account frozen particles to calculate temperature of the system, what, i think, gromacs does. If you still have concerns, there is a way to figure it out of a simple test. E.g. generate a simulation system with two point particles. Freeze one particle, assign velocity to another one, evaluate temperature by mdrun, then unfreeze the first particle, check if it has a zero velocity, evaluate temperature by mdrun. If the temperature displayed by mdrun drops down in the second evaluation, then you were correct. S. Alireza B wrote > The output configuration of my system shows that all of my solid phase has > melted. So, no crystallization occurred. Sorry, the output after 0.5 ps of simulation time in NVE shows complete melting? If it is true, that this illustrates that your crystal phase is really far from equilibrium with respect to internal degrees of freedom (has high potential energy). When you unfreeze this in your NVE simulation the potential energy tends to decrease, and the only way for it to decrease is to transform into kinetic energy (which increases), leading to increase of temperature. -- View this message in context: http://gromacs.5086.n6.nabble.com/Anomaly-in-Temperature-Behavior-tp5004808p5004843.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
