[gmx-users] Re: velocities (gmx-users Digest, Vol 29, Issue 60)

[Prasad Gajula]

Thanks for your answer. I hope I did not catch your points well.

So, you mean I can  use 'gen_vel = no'  for the md runs (MD without
position restraints, after the completion of PR run with position
restarints)
my procedure as follows......

EM ---> PR(300ps @ 300K) ----> MD (30ps @ 80K. no postion restraints)--->
MD (30 ps @ 100K, no postion restraints ) ---> MD (30 ps @ 200K, no
postion restraints) ----> relaxation MD(250ps @ 300K, no postion
restraints) ----> final MD (300K, no postion restraints)

After Energy minimization, I apply position restarints and generate new
velocities at 300K. I take the output of PR run as input to the next MD
run which started at 80K ( no position restraints from now). And also from
here onwards i dont generate any new velocities, but with the velocities 
which are written in the previous runs.
Please let me know if iam correct or not.
Thanks again
Gajula
> 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