[gmx-users] Using thermostats to create temperature gradient in system

[Suzen, Mehmet]

Hi Agnivo,

Temperature gradient means non-equilibrium MD (NEMD)

See notes from Prof. Martini:
https://nanohub.org/resources/7582/download/Martini_L10_NonequilibruimMD.pdf

What observable would you like to measure? Lets say you want to
measure observable A.

One "procedure" I can think of:

1.  You can run all system at T=300K with NVT. After equilibrium,
continue running all system at T=400K with freezing solvent group.
See, to how to freeze a group,
http://manual.gromacs.org/online/mdp_opt.html#neq

To get a good statistic, you need to repeat this procedure K times as
"solvent thermal wall" configuration  would be
different at each simulation.

100ps? Where did you get that? You need to see how observable A
behaves to see if 100ps is enough, <A> time average. And see how <A>
behaves in K different cases.


2. Similar to previous procedure but this time after freezing solvent
group, run system in NVE. Again, you need to repeat this
many times to get a good statistic. Similarly monitor observable A to
see if 500ps is enough.

However,  I suggest you to talk to someone having NEMD experience as
this procedure is just a heuristic approach.

-m