[gmx-users] Creating a temperature gradient in water

[Alex]

I would like the asker to seriously read into what Mark has suggested to
help reduce the number of published papers with various degrees of setup
nonsense.
Mark's restraint strategy readily accomplishes the gradient, but creates
two partial "pistons" at the thermal boundaries due to restraints. If I was
to go for this, I'd use a really wide box. A really wide one.

Alex

On Tue, Jan 10, 2017 at 9:57 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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