Temperature of system not attained to desired set value

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1

GROMACS version: 18.5
GROMACS modification: No
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I have set temperature of my system to 305 K, during the NVT and NPT equilibration run, system attained 305 K, but during production run, system attained temperature of 314 K even though value is set at 305 K. Couldn’t figure out why this is happening. Please help.
files:
md.mdp (2.2 KB)
npt.mdp (2.2 KB)
nvt.mdp (2.2 KB)

Temperature

2

You mdp parameters seem reasonable.

What kind of system is this?

3

Thank you Berk Hess for the reply.

This is stack of three lipid bilayers one above other. Without any water. There are three types of molecules in bilayer. I have highlighted head atoms with red, to highlight bilayer boundary, it is not different molecule.
image

4

I assume you quickly get the incorrect temperature, right?

Could you check if you get the same issue with the 2021 version?

5

Yes, somewhat quickly, temperature increased within first 100 ps.

image
image889×264 16.1 KB

Here in figure, with blue color, I have shown last 40 ps of equilibration run (using npt.mdp) and then with continuation = yes in md.mdp, I am further extending the simulation.

Sure, I will try 2021 version, and get back to you.

Thanks.

6

You have a nasty resonance with a period of about 2.4 ps in your system. My guess is that this is due to the second order Parrinello-Rahman pressure coupling coupling to some vibrational mode in your system. You have tau_t set to 5 ps, but your compressibility will be off from the one of water, as you have a pure membrane system. So I guess your actual tau_t is around 2.4 ps. You can try tau_t is 10 or 20 ps and see if that removes the resonance. Even better would be using the c-rescale barostat that we added in the 2021 version of GROMACS.

7

Thanks Berk Hess for the solution, it worked!

I tested both suggestions, tried tau_p = 10 with PR pressure coupling and tau_p = 1 with c-rescale pressure coupling. In both cases, system temperature equilibrated around set temperature.

Thanks again
-Yogesh