VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Apr 30 2020 - 07:45:14 CDT

Hi Doug,

In order to build the initial solvent box, I do something like what was
described here for a box of methanol:
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/29596.html

Then in general you'd do something like this, where the -ks argument is the
atomselection text you'd use to grab a single atom from the solvent
molecule ("name CB" is what I use for methanol).

solvate input.psf input.pdb -o output -spdb solvent.pdb -spsf solvent.psf
-stop solvent.top -ws 2.4 -ks "name CB"

Mixed solvents are tricky though. What I have done in the past is to use
the -minmax argument to fill my solvent box by volume, and let the solvent
mix during equilibration. The solvate plugin to my knowledge cannot deal
with mixed solvents directly, because the -ks argument needs to resolve to
a single atom in the molecule.

-Josh

On Thu, Apr 30, 2020 at 5:50 AM HOUSTON Douglas <DouglasR.Houston_at_ed.ac.uk>
wrote:

> Hi all,
>
> I'm hoping to do simulations of peptides in 25:75% TFE:water using the
> CHARMM36m forcefield. I understand that solvation of a system using
> nonstandard solvent is possible, but I'm struggling to understand just how
> to go about it.
>
> I see the instructions here:
>
> https://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
>
> But I'm unsure as to the steps I need to take. I'm particularly confused
> about what the -ks flag is doing, and how I make the initial "cubic box of
> the solvent of choice".
>
> Can someone please direct me to step-by-step instructions? Is there a
> tutorial on this somewhere?
>
> Thanks in advance.
>
> Doug
>
>
>
> The University of Edinburgh is a charitable body, registered in Scotland,
> with registration number SC005336.
>