[gmx-users] about simulation of small molecules in vacuum. link to dropbox

[lazaro monteserin]

Dear all

I am trying to simulate in Gromacs 2020.1 small molecules nucleosides (32
atoms) in vacuum. I have try to follow the tutorial steps, so I created a
box and followed did an energy minimization. But the graph from
potential.xvg doesn't look similar to the ones on the tutorials. Somebody
could guide on how to do this kind of simulation properly? or if I am doing
things right?

This is the link to the files minim.mdp, potential.xvg and .top related to
my simulations in vacuum in dropbox:

Kindly,
Lazaro

vacuum_MD
Abrir el vínculo en Dropbox
<https://www.dropbox.com/sh/yu0lj8dit6vwltz/AACo5Kmw45uUE5yTDHPceekDa?dl=0>