[gmx-users] Queries regarding temperature gradient

Sun Jul 8 20:39:46 CEST 2018

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

==================================================