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

[lazaro monteserin]

Dear Dr. Lemkul thank you very much for your answer.

I will look on the literature.

El lun., 13 de abr. de 2020 a la(s) 12:55, Justin Lemkul (jalemkul at vt.edu)
escribió:

>
>
> 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
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
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