[gmx-users] Recommended protocol for cooling down temperature in 50 K steps

[Andrew DeYoung]

Hi, 

I have a system that I would like to equilibrate in the NPT ensemble at high
temperature, and then, in subsequent equilibration steps, cool down in steps
of 50 K.  Thus, in the first step, I will use "gen_vel = yes", while in all
subsequent steps, I will use "gen_vel = no".

Suppose that I want to run 200 ps at 700 K, 200 ps at 650 K, and 200 ps at
600 K.  I have two possible protocols, Protocol 1 and Protocol 2.  If you
have time, can you please help me see what is the difference between these
two protocols?  For my application (cooling down a system in steps of 50 K),
which protocol do you think is more appropriate?  Or do you have any other
suggestions?  

In Protocol 1, both the output configuration (.gro) and the checkpoint
(.cpt) resulting from mdrun of the previous step are fed to grompp of the
next step (however, I am not appending files, because I want separate .trr
files for each step):  

***BEGIN PROTOCOL 1***
STEP 1 (700 K, 200 ps):
grompp -f a1.mdp -c inputconf.gro -p topology.top -o a1.tpr -po a1out.mdp
;where a1.mdp contains "gen_vel = yes"
mdrun -deffnm a1 -cpo a1.cpt -noappend

STEP 2 (650 K, 200 ps):
grompp -f a2.mdp -c a1.gro -p topology.top -t a1.cpt -o a2.tpr -po a2out.mdp
;where a2.mdp contains "gen_vel = no"
mdrun -deffnm a2 -cpo a2.cpt -noappend

STEP 3 (600 K, 200 ps):
grompp -f a3.mdp -c a2.gro -p topology.top -t a2.cpt -o a3.tpr -po a3out.mdp
;where a3.mdp contains "gen_vel = no"
mdrun -deffnm a3 -cpo a3.cpt -noappend
***END PROTOCOL 1***

In Protocol 2, only the output configuration (.gro) resulting from mdrun of
the previous step are fed to grompp of the next step:

***BEGIN PROTOCOL 2***
STEP 1 (700 K, 200 ps):
grompp -f a1.mdp -c inputconf.gro -p topology.top -o a1.tpr -po a1out.mdp
;where a1.mdp contains "gen_vel = yes"
mdrun -deffnm a1

STEP 2 (650 K, 200 ps):
grompp -f a2.mdp -c a1.gro -p topology.top -o a2.tpr ;where a2.mdp contains
"gen_vel = no"
mdrun -deffnm a2

STEP 3 (600 K, 200 ps):
grompp -f a3.mdp -c a2.gro -p topology.top -o a3.tpr ;where a3.mdp contains
"gen_vel = no"
mdrun -deffnm a3
***END PROTOCOL 2***

Which is preferable?  In both protocols, the end velocities of the previous
step are used to begin the next step, since the .gro files contain the
velocities.  However, only in Protocol 1 do I use the checkpoint files to
continue the run.  Does doing so just cause the energy statistics to be more
consistent between steps?

Also, if you have time, should I use "continuation = yes" in a2.mdp and
a3.mdp?  My system does not have any constraints per se; atoms are either
frozen (using a freeze group to simulate an immobilized surface) or their
bonds are flexible.  Thus, I am not really using any constraints, unless
freeze groups count as constraints.  However, I am not sure what this means
as far as what to set "continuation" to in a2.mdp and a3.mdp.

Thank you very much for your time!

Andrew DeYoung
Carnegie Mellon University