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

[lazaro monteserin]

The simulation ends without error. I am going to attach the files in
Dropbox or google drive and send them in that format. Thank you for the
guidance

On Sun, Apr 12, 2020 at 1:42 PM John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> 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
>
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