[gmx-users] Queries regarding temperature gradient

Sabreen Farnaz s.neelima531 at gmail.com
Fri Jul 6 19:07:24 CEST 2018

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?

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).
> 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)
> Should gen_temp have the same temperature values in each of nvt and md mdp
> files?
> Please help.
> Thank you!
> Regards,
> Neelima S.

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