[gmx-users] velocities

[Mark Abraham]

Prasad Gajula wrote:
> Dear Gromacs Users,
> 
> I am getting different results for simulations with " gen_vel=yes"  and
> "gen_vel= no".

This is expected. No two simulations will be the same unless you run 
then on the same hardware with exactly the same inputs. gen_vel requires 
the use of a random number seed. What you want to do, is after 
equilibration, be sampling from the correct ensemble.

> I have generated velocities only for PR MD at 300K. after that I set '
> gen_vel= no ' in mdp file.  After the position restrained MD , I slowly
> increased the temparature from 80K , 100K , 200K and last 300K. (with
> 'gen_vel=no' for all MD)
> Is it correct? Because I read both 'yes' and 'no' as possibilites in some
> references. Iam bit confused which to use for exact simulations.

Personally, I don't think the practice of velocity reassignment in 
incremental heating while using position restraints is demonstrably 
better than not using reassignment in incremental heating.

Mark