VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Jul 30 2020 - 15:44:22 CDT

Dear Raman,
Please see below.

On Thu, Jul 30, 2020 at 4:17 PM Raman Preet Singh <
ramanpreetsingh_at_hotmail.com> wrote:

>
>
> 1. For creating a pdb and psf of the solvent box, I need to
> equilibrate the box of solvent (or solvent mixture). For how long (10 ns or
> more?) and using which ensemble (NPT?) should equilibration be performed?
>
> For most cases, an NPT equilibration would suffice, for long enough for
key thermodynamic parameters (average pressure, temperature, volume,
energy) to stabilize

>
> 1.
> 2. Can the box size of the solvent be different (smaller or larger)
> from the box size of the final system (protein + solvent)? If yes, then how
> much difference is acceptable assuming that the final box size will be
> 50x50x50 angstrom.
>
> Yes, it can be. Solvate will tile your solvent box through space as
needed. I would recommend a 20 or 30 Angstrom side length on the box that
you equilibrate.

>
> 1.
> 2. When a protein is inserted in the equilibrated solvent box, the
> protein will displace the solvent resulting in an increase in pressure--0000000000006a840005abaebdfc--