[gmx-users] Wrong pressure with rigid water

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 15 08:58:32 CET 2016


The solvent models are designed to be rigid, use flexible versions only if
you know why they will be a good model for you.

Measuring pressure can take nanoseconds, but we don't have enough
information to know what you've done and its error estimates.


On Mon, 14 Nov 2016 17:21 Sudip Das <das.sudip37 at gmail.com> wrote:

> Dear All,
> I am simulating a protein in water with GROMOS96 force field (gromos54a7)
> and SPC/E water model. After minimization followed by NVT equilibration, I
> performed 2ns of NPT equilibration. From the converged box length I have
> taken the average value and set the box length (in npt_equilibrium.gro
> file) to that value and used this for NVT production run.
> In the production run, temperature, potential and total energies are
> reasonable, whereas the pressure is behaving weirdly. I have started the
> NVT production run with 1 bar pressure.
> NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to 5
> bar
> NVT production run with rigid water: P = 750 to 780 bar
> Did anyone encountered this kind of problem? I would appreciate your kind
> help in resolving this.
> Best regards,
> Sudip
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