Hi Loris, It may be better to have ld_seed=-1. This way, you won't have the same seed again when you restart.
@Article{Cerutti2008, author = "Cerutti, D S and Duke, R and Freddolino, P L and Fan, H and Lybrand, T P", title = {Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics}, journal = "J Chem Theory Comput", year = "2008", volume = "4", pages = "1669-1680" } Best regards, Ran Loris Moretti wrote: > 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 > > -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman ------------------------------------------------------
_______________________________________________ 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