Sabreen Farnaz s.neelima531 at gmail.com
Sun Jul 8 20:21:56 CEST 2018

```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,
> > 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!
> >> 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 doesn't make much sense to me.
> >>
> >> -Justin
> >>
> >>>> 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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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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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> Gromacs Users mailing list
>
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```