[gmx-users] PMF and lack if NPT equilibration

[Alex]

Dear gromacs user,

In a PMF simulation of a short peptide on solid surface, I am using the
"direction-periodic" as "pull-coord1-geometry" in the Z  direction, then as
you know the equilibration of the system in NPT ensemble is not doable for
the individual windows. So, for each windows of umbrella sampling, I am
going to do minimization and NVT equilibration and then MD production. I
was wondering if the lack of the NPT  equilibration would not badly affect
on the result PMF? If so, how can I compensate it somehow?

By the way, I nicely minimized. equilibrated (both NVT and NPT) and a 60 ns
of production simulation of my initial system before coming to the pulling
step.

Thanks.

Regards,
Alex