[gmx-users] Queries regarding temperature gradient

Justin Lemkul jalemkul at vt.edu
Fri Jul 6 20:00:53 CEST 2018

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 doesn't make much sense to me.


>> 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


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