VMD-L Mailing List

From: HOUSTON Douglas (DouglasR.Houston_at_ed.ac.uk)
Date: Thu Apr 30 2020 - 06:17:23 CDT

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

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