Dear Mark and Oscar, Thanks for your help! I checked the velocity distribution and the velocity at different simulation frames. As you said the initial velocities are all set to zero and at the next step are already changed, I also guess by the random thermal noise.
Thus, my idea of simulating the same system with different random generator number for thermal noise (ld_seed) might account for a small variation of the "initial" conditions? loris... In message <8c3f24a40903110611j4f69c75emb0f5eef0484de...@mail.gmail.com> Discussion list for GROMACS users <gmx-users@gromacs.org> writes: > > > > Thus I am a bit confused about it! > >> > > > > I'm confused about the manual comment about only being meaningful with the > > MD integrator, but we 'll have to wait until someone who knows something > > about LD can post! > > > For LD, the velocities will (should) get rescaled by the random thermal > noise, that is- by the Langivin thermostat. > With MD, the thermostat works like friction (positive or negative friction). > So you see, that for LD, an initial velocity of zero should next be changed > by the thermostat, while for MD the rescaling shouldn't work for zero. > > --Omer Markovitch. > > Koby Levy research group, > Weizmann Institute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
