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

[John Whittaker]

Hi Lazaro,

> 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?

No idea without more information. Does the simulation end with or without
an error?

>
> Should I modified the .mdp?

We have no way to tell if you don't post the contents of your .mdp file.

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

The mailing list does not accept attachments - You have to upload the plot
to an external hosting site (google drive, dropbox, etc...) for us to be
able to see it.

>
> Appreciating any help in advance
>
> kindly,
>
> Lazaro
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----------------------------------------

John Whittaker
Ph.D. Candidate
Department of Mathematics and Computer Science
Freie Universität Berlin

+49 0160 936 04221