[gmx-users] Creating a temperature gradient in water

[Mark Abraham]

Hi,

Yes, as Alex says, you can get something done, but whether it is a
reasonable model of reality is another matter. Having the "bath" groups at
even wider temperature ranges, and analyzing only a subset of the data
could help mitigate end effects from whatever regime generates the
gradient. I would read carefully, and plan how I'm going to show my
simulation is a model, and not just a computation :-)

Mark

On Tue, Jan 10, 2017 at 8:00 PM Alex <nedomacho at gmail.com> wrote:

> 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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