[gmx-users] Equilibration using position restraints in NPT

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 9 04:41:31 CEST 2017

On Sun, Oct 8, 2017 at 11:30 PM Neha Gandhi <n.gandhiau at gmail.com> wrote:

> Thank you Mark.
> The nanotube is 2x2x13 nm long. Then I use editconf with -c  and -d  2 and
> solvate using spc216.gro.

Please visualize that result. Such a command would put solvent all around
your nanotube, so it could not have an infinite topology and be stable.

How can I calculate box size after NVT so that I get density of 1 or 0.99
> when using pressure coupling?

Your z dimension is chosen by the size of the nanotube. Your x and y might
be chosen by whatever the above procedure suggests, but you can't actually
use the box that it produced.


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