Re: [gmx-users] initial velocities Langevin dynamics

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 Langevi

Re: [gmx-users] initial velocities Langevin dynamics

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

Re: [gmx-users] initial velocities Langevin dynamics

> > 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, th

Re: [gmx-users] initial velocities Langevin dynamics

Loris Moretti wrote: 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) Well it is much more effective to say that the first time. :-) Getting someone's att

Re: [gmx-users] initial velocities Langevin dynamics

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 veloc

Re: [gmx-users] initial velocities Langevin dynamics

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 no

[gmx-users] initial velocities Langevin dynamics

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

[gmx-users] initial velocities Langevin dynamics

Hi there, 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