Berendsen pressure coupling

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Dear all,

I have to use position restraint for a small part of the system

After 20 ns of NPT equilibration, for the production run, I got the following :

NOTE 2 [file, line 59]:
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.

Number of degrees of freedom in T-Coupling group Protein is 66273.00
Number of degrees of freedom in T-Coupling group non-Protein is 450122.00

NOTE 3 [file testrun.mdp]:
Removing center of mass motion in the presence of position restraints
might cause artifacts. When you are using position restraints to
equilibrate a macro-molecule, the artifacts are usually negligible.

WARNING 1 [file testrun.mdp]:
You are using pressure coupling with absolute position restraints, this
will give artifacts. Use the refcoord_scaling option.

Why does Berendsen pressure coupling work but the other doesn’t? can I safely use Berendsen pressure coupling for the production run?

Thank you so much

You should not use a Berendsen barostat. Use c-rescale instead, which behaves like Berensen, but produces the correct ensemble.

Note the warning that you might be strange artifacts when scaling the who box while keeping some atoms restrained to absolute locations. I suggest to follow the suggestion given in the message.