[gmx-users] Constant Density

Nash, Anthony a.nash at ucl.ac.uk
Tue Apr 26 15:43:56 CEST 2016

Hi all,

At the risk of bending the rules of thermodynamics, I¹m wondering whether
Gromacs can maintain density of a water box (0.750 g/L density of water in
a collagen fibril environment) whilst applying an NPT ensemble?

gmx_d solvate, fills up to 2/3 of my truncated oct cell, with my protein
at the centre. An NVT simulation does not redistribute the water. To do
this I need to perform an NPT run, but even so this rapidly shrinks the

I have considering looking up the necessary pressure value for this
density, however I¹m a bit uncertain whether this maintains any
physiological realism for the protein itself.

I¹ve tried googling with little success.

Any thoughts are appreciated.

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