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 <49B792A4.3070108@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
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