[gmx-users] Problem with T-coupling.

[Udaya Dahal]

Hi,
I was simulating the PPO, n=27 chain in water. Currently I am simulating
only single chain and so far the phase behavior and he h-bond looks good
for the higher temperature but as I go to the lower temperature (293K and
298K), I expected to get little extended  structure unlike the coiled
structure at higher temperature.

But the problem, I am facing here is not the conformation but the overall
simulation. I changed from berendsen T-coupling to nose-hoover and
berendsen P-coupling to Parrinello-Rahman pressure coupling. When I see the
trajectory in VMD, the trajectory of Berendsen thermostat and barostat
looks like liquid but the nose-hoover and Parrinello-Rahman looks like
freezing for the same system.
When i checked the temperature from g_energy, it shows the coupling
temperature. Could you please tell me what's wrong in the simulation?
I have attached the .mdp file here with the email in google drive.​
 eq.mdp
<https://docs.google.com/file/d/0ByXdaXpbCwOyUVJuOFZ4dFBaa1U/edit?usp=drive_web>
​This one is for Berendsen T coupling.

​
 eq_nh.mdp
<https://docs.google.com/file/d/0ByXdaXpbCwOySnBIa2tLRkFPZGc/edit?usp=drive_web>
​This one is for Nose-hoover.


-- 
Udaya Dahal,
Graduate Assistant,
Department of Physics,
University of Connecticut