[gmx-users] GROMACS automation

Mohamed Abdelaal m.b.abdelaal at gmail.com
Thu Mar 12 12:35:13 CET 2020


I was planning to put the velocities in the .gro file from which I am
inserting the molecules. If the gmx insert-molecules will ignore the
velocities of the atoms, can you please guide me how can I insert the
molecules with a velocity ?
I have read a paper which mentions that they inserted the molecules  and
the velocities of the ATOMS were sampled from a distribution with standard
deviation =xx and mean = xxx.


On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote:
> > I want to insert an atom with a velocity moving downwards toward the
> > graphene sheet in my box.
> > Yes I need to remove any atom moving away from my substrate or the
> > deposited atoms and far by 0.4 nm.
> > Then repeat the process until I have inserted 3000 atoms.
>
> gmx insert-molecules has no knowledge of velocities, and atoms are not
> inserted with any velocity, only a position.
>
> Removal of atoms is handled with gmx trjconv and a suitable index file
> generated by gmx select (in this case, since you're specifying a
> geometric criterion).
>
> -Justin
>
> > Thanks for your reply.
> > Mohamed
> >
> > On Wed, Mar 11, 2020 at 13:43 John Whittaker <
> > johnwhittake at zedat.fu-berlin.de> wrote:
> >
> >> Write a script that calls gmx insert-molecules 3000 times and uses the
> >> previous output as input for each call.
> >>
> >>
> >>
> http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html
> >>
> >> Is there something you have to do in between each insertion?
> >>
> >> - John
> >>
> >>> Hello everybody,
> >>>
> >>> I am trying to insert molecules into a box but I have to insert one
> >> single
> >>> molecule at a time reaching 3000 molecule in total. Is there a way to
> >>> automate this process ?
> >>>
> >>> Thanks
> >>> Mohamed
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>
> Justin A. Lemkul, Ph.D.
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