[gmx-users] Queries regarding temperature gradient

Sun Jul 8 20:49:03 CEST 2018

That makes sense.
Thanks a lot, lot for your help.

On Mon, 9 Jul 2018, 00:40 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 7/8/18 2:37 PM, Sabreen Farnaz wrote:
> > I had read this part from gmx help traj "plots temperature of each group,
> > provides velocities are present...no corrections are made for constraines
> > degrees of freedom..."
>
> And therein lies the difference. gmx energy has the correct number of
> degrees of freedom, gmx traj has no knowledge of such information,
> meaning you have to perform a correction on its resulting temperature.
>
> -Justin
>
> > Looks like it uses Kinetic energy from velocity to calculate the
> > temperature. My question is, is it supposed to be different than that
> > calculated by gmx energy? It is to be noted that in my case the
> temperature
> > calculated by gmx energy after production run is same as that specified
> in
> > nvt/npt steps. But temp from gmx traj is much less.
> >
> > Thanks a lot for your help.
> >
> > On Mon, 9 Jul 2018, 00:26 Mark Abraham, <mark.j.abraham at gmail.com>
> wrote:
> >
> >> 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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> --
> ==================================================
>
> 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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