Dear Mark, Thanks for answering! My question arises because in the manual is also reported that gen_vel "is only meaningful with integrator md" (mdp options section: velocity generation) and because I provide a .gro file with no velocities and I clearly specify in the .mdp not to generate velocity.
Thus I am a bit confused about it! loris... In message <49b792a4.3070...@anu.edu.au> Discussion list for GROMACS users <gmx-users@gromacs.org> writes: > Loris Moretti wrote: > > Hello everybody, > > > > Sorry to post again the same question but I've got no answer so far. > > > > I have a technical question, it might be silly but I couldn't find an > > answer so far. How are assigned the initial velocities for the particles > > when Langevin dynamics is performed? > > > > In normal MD the gen_vel/gen_seed are used for random generation of the > > initial velocities. I am used to vary this number with the same system in > > order to explore the effect of different initial conditions. I was > > wondering if there is such a possibility with Langevin dynamics, like > > changing the ld_seed number? > > As you'll see in the manual (section 7.3.4) ld_seed is not used for > generating velocities. I expect gen_vel and gen_seed do this, since the > purpose of generating initial velocities doesn't change with the > integrator. You're still wanting to sample a Maxwell distribution, no? > > You could have experimented with gen_seed and used gmxcheck to compare > pairs of .tpr files to answer your own question. > > Mark > _______________________________________________ > 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 _______________________________________________ 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
