Mark.Abraham at anu.edu.au
Tue Sep 19 03:31:19 CEST 2006
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.
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