[gmx-users] how to run a MD of a small molecule in vacuum in Gromacs

[lazaro monteserin]

Hi, my name is Lazaro.  I have done calculations using QM methods. But I am
starting now to learn MD and I am using Gromacs 2020.1. I want to run
simulations in vacuum for small  deoxynucleosides and ribonucleosides
(around 32 atoms) with the finality to initially optimize these molecules
relaxing all position (find the most stable structure) to use this
structure as input for DFT calculations in the future.

I have study from the manual and the
gromacs.org_gmx-users at maillist.sys.kth.se tutorials and have successfully
run a couple of simulations of the adenosine in water environment.

But when I try to run the simulation in vacuum I have some problems. If I
create a box, but from there instead of fill it with water I go directly
and try to do an energy minimization, when I visualize the potential it
decrease but the curve does not look like the examples or like when I do
the simulation in vacuum.

Do you think this is correct? or is correct how I am proceeding?

Should I modified the .mdp?

I am attaching an image of the potential energy minimization from xmgrace.

Appreciating any help in advance

kindly,

Lazaro