[gmx-users] how to run equilibration when freezing part of an small molecule in vacuum and in water environment?

[Justin Lemkul]

On 4/13/20 10:37 AM, lazaro monteserin wrote:
> Dear Gromacs users
>
> I have three questions about the details of running MD of small molecules
> in gromacs:
>
> 1) If I run a MD in vacuum if I freeze part of the nucleoside (lets say the
> carbons in the sugar) with genrestr, should I use temperature coupling
> groups?

Freezing and restraining are different; don't use the terms 
interchangeably. Freezing means the atoms are never updated (position or 
velocity), and I don't recommend using this approach as it is entirely 
unphysical. What you're talking about is applying a restraint. You need 
to assign all atoms to a temperature-coupling bath. If you don't, that's 
also completely unphysical.

> 2) Now, if I freeze in the nucleoside again the carbons from the sugar but
> the calculation is in water, should I use temperature coupling?, should I
> put the nucleoside in one group and the solvent in another group? What
> temperature coupling methodology would be more recommended?

For a small solute in water, couple the whole system together.

> 3) For these type of small molecules (around 32 atoms) what would be the
> best time to run the MD, e.x. 5ns, 10ns, 20ns, etc?

You should base this conclusion on your examination of the literature. 
What are the time scales of the dynamics you are interested in? What 
have previous studies on similar systems demonstrated?

-Justin

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Justin A. Lemkul, Ph.D.
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