[gmx-users] Creating a temperature gradient in water

[Mark Abraham]

Hi,

Naturally one can only have a monotonic gradient over half of a periodic
direction of a simulation cell, ie between two themostatted groups. Also,
if you rely on the temperature coupling groups to implement that, then
these are fixed at grompp time, so diffusion will tend to wreck the intent.
One could either use (flat-bottomed?) position restraints to keep the two
groups localized, or periodically stop the simulation and use gmx select to
re-create index groups with the desired spatial locality. Obviously, the
remaining water should not be coupled to a thermostat.

Mark

On Tue, Jan 10, 2017 at 5:44 PM Alex <nedomacho at gmail.com> wrote:

> Erik,
>
> Even with PBC, something like Ibrahim's scenario is possible in principle
> (T_1 in the region at the center of the box, T_2 at the edges). However,
> can this geometry-based thermostatting for fluids be accomplished in GMX?
>
> Alex
>
> On Tue, Jan 10, 2017 at 8:15 AM, Erik Marklund <erik.marklund at kemi.uu.se>
> wrote:
>
> > Dear Ibrahim,
> >
> > Do you use pbc? If so, how does that work with your gradient?
> >
> > Kind regards,
> > Erik
> >
> > > On 10 Jan 2017, at 15:00, ibrahim khalil <
> ibrahim.khalil.chem at gmail.com>
> > wrote:
> > >
> > > Dear gromacs users,
> > >
> > > I have a simulation box containing nothing but water (TIP3P). I want to
> > > create a temperature gradient within water (ie. 300K in the left side
> and
> > > 500K in the right side of the simulation box).
> > >
> > > I have successfully applied different temperatures to different groups
> in
> > > my other simulations (for example, different temperatures for water and
> > > proteins).
> > >
> > > How can apply different temperatures within the same group of liquids
> (in
> > > my case, water)?
> > >
> > > Thanks in advance.
> > > --
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