[gmx-users] Queries regarding temperature gradient

[Mark Abraham]

Hi,

gmx help traj has a useful point to make about how it estimates temperature
from the velocities.

Mark

On Sun, Jul 8, 2018 at 8:22 PM Sabreen Farnaz <s.neelima531 at gmail.com>
wrote:

> Thank you, Dr. Lemkul. I have done this but used gmx energy to find the
> temperature of each frame (defined as separate energy groups) in place of
> gmx traj.
> Can you please elaborate what is the difference between the temperature
> calculated by these two commands? (gmx energy and gmx traj) I have found
> different values for the same energy group using them.
>
> On Mon, 9 Jul 2018, 00:10 Justin Lemkul, <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 7/6/18 4:30 PM, Sabreen Farnaz wrote:
> > > Dear Dr. Lemkul,
> > > Thank you for your answer. Can you please also advise how can I get the
> > > temperature of a system as a function of distance using gromacs 5.1.5?
> > gmx
> > > energy plots the temperature of the centre of mass of energy groups
> > against
> > > time. gmx traj also does the same from velocity information.
> >
> > If it can even be done, it will be very time-consuming. You'd have to
> > run gmx select on each frame of the trajectory to specify a selection of
> > atoms that falls within some region of space. With that index group,
> > you'd have to use gmx traj to extract the velocities of that selection
> > in that frame, then compute the temperature. Then repeat that for every
> > slice in every frame, each individually, since most tools do not yet
> > support dynamic selections.
> >
> > -Justin
> >
> > > Regards,
> > > Neelima S.
> > >
> > > On Sat, 7 Jul 2018, 00:01 Justin Lemkul, <jalemkul at vt.edu> wrote:
> > >
> > >>
> > >> On 7/6/18 1:07 PM, Sabreen Farnaz wrote:
> > >>> Dear all,
> > >>> This is in regard to my previous queries. The warning in NVT step can
> > >>> possibly be ignored using -maxwarn but I am still not sure about the
> > >> rest!
> > >>> Can someone please help?
> > >> tau_t = -1 means temperature coupling is not applied. Whether that's
> > >> what you want or not is up to you, but in that case, your ensembles
> are
> > >> not NVT or NPT, because T is no longer conserved.
> > >>
> > >>> Thanks,
> > >>> Neelima S.
> > >>>
> > >>> On Fri, 6 Jul 2018, 01:56 Sabreen Farnaz, <s.neelima531 at gmail.com>
> > >> wrote:
> > >>>> Dear all,
> > >>>>
> > >>>> I am setting up a system where I want the solute to be immersed in a
> > >>>> solvent with a temperature gradient. I have defined two different
> > >>>> temperature groups, two portions of the solvent, and want them to be
> > at
> > >> say
> > >>>> T1 and T2 kelvins. The rest of the system will not be subjected to a
> > >>>> thermostat  (tau_t=-1).
> > >> Realize that with PBC, you're not likely to get what you want. I don't
> > >> know how you're defining the T1 and T2 groups, but if they're in
> contact
> > >> via PBC, the "gradient" really doesn't exist - you have a hot and cold
> > >> bath directly in contact. See previous threads on temperature
> gradients
> > >> for more discussion. If the T1 and T2 groups are capable of diffusing,
> > >> then you definitely don't have a gradient.
> > >>
> > >>>> My questions are:
> > >>>> 1. Should NVT and NPT mdp files also have the same t_ref and tau_t?
> A
> > >>>> tau_t=-1 gives a warning in nvt grompp, can it be ignored?
> > >>>> 2. I am generating velocities in nvt run and continuing npt with
> > >> previous
> > >>>> velocities. For production run, I only take the equilibrated
> structure
> > >> and
> > >>>> generate velocities again. (No continuation)
> > >> If you're re-generating velocities, what was the point of the previous
> > >> equilibration steps? You're just re-setting your system to a random
> > state.
> > >>
> > >>>> Should gen_temp have the same temperature values in each of nvt and
> md
> > >> mdp
> > >>>> files?
> > >> If you intend to model the same ensemble, yes, but again re-generating
> > >> velocities after equilibrating does
> <https://maps.google.com/?q=%0A%3E+%3E%3E+velocities+after+equilibrating+does&entry=gmail&source=g>n't
> make much sense to me.
> > >>
> > >> -Justin
> > >>
> > >>>> Please help.
> > >>>> Thank you!
> > >>>>
> > >>>> Regards,
> > >>>> Neelima S.
> > >>>>
> > >> --
> > >> ==================================================
> > >>
> > >> Justin A. Lemkul, Ph.D.
> > >> Assistant Professor
> > >> Virginia Tech Department of Biochemistry
> > >>
> > >> 303 Engel Hall
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at vt.edu | (540) 231-3129
> > >> http://www.thelemkullab.com
> > >>
> > >> ==================================================
> > >>
> > >> --
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> > >>
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.thelemkullab.com
> >
> > ==================================================
> >
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