Choice of Barostat during NPT equilibration

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No

Hi,

I am trying to simulate a protein-ligand complex embedded in the POPC bilayer. I have generated my system using CHARMM-GUI. While I am trying to start the for NPT equilibration of my system I am getting the following NOTE from Gromacs:

NOTE 2 [file topol.top, line 34]:
You are combining position restraints with Parrinello-Rahman pressure
coupling, which can lead to instabilities. If you really want to combine
position restraints with pressure coupling, we suggest to use Berendsen
pressure coupling instead.

After some reading online I understand that Berendsen pressure coupling might not be the appropriate way to proceed.

I am using the following settings in my mdp file:

tcoupl = Nose-Hoover
tc_grps = Protein_GDS_POPC Solvent
tau_t = 1.0 1.0
ref_t = 303.15 303.15
;
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 5.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
refcoord_scaling = com

I have gone through multiple tutorials available on the internet. I see mostly Parrinello-Rahman pressure coupling is used (including the one in tutorial written by @jalemkul . I am a bit confused and need some advice.

Thanks in advance

2

When the system is not in a well-equilibrated state, a second order pressure coupling such as Parinnello Rahman can not be used. C-rescale will be most appropriate one. I don’t know C-rescale is available on your Gromacs version since C-rescale is very new.

3

Hi Dulaj

Many thanks for replying to my post. I did not mention (and I am sorry for that) in my earlier post that I already did around 5 ns of NVT equilibration with my system. My system is fairly stable with no warnings or collapse. Its just that I have the position restrains turned on.

So according to your suggestion can I modify the follows in my mdp file:

pcoupl = C-rescale
pcoupltype = semiisotropic

Thanks