[gmx-users] Constant Density
Smith, Micholas D.
smithmd at ornl.gov
Tue Apr 26 18:00:51 CEST 2016
One possible way I can think of to get the water to redistribute is to perform some temperature annealing of just the solvent, i.e. raise the temperature every so many steps to a max ~500K then quickly quench (lower the temperature) the solvent back to the physiological regime. Repeat this a few cycles to make sure you've redistributed the water as you expect. Just make sure to hold the protein fixed with restraints. After it has done a few cycles (maybe 5 or so), try running with NVT at the proper temperature for both protein+solvent (typical NVT simulation). You should note that the water will not remain "uniformly" distributed; though, as it will tend toward its equilibrium values so your system should be considered non-equilibrium MD (thought the extent of how long it takes to relax to the standard state, may allow you to approximate it as quasi-equilibrium)
There may be other ways to do this as well.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nash, Anthony <a.nash at ucl.ac.uk>
Sent: Tuesday, April 26, 2016 9:29 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Constant Density
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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