[gmx-users] GROMACS automation

Thu Mar 12 13:10:21 CET 2020

The paper information is as below :
Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic
Light-Emitting Diode Films
Authors: Claire Tonnel + , Martin Stroet + , Bertrand Caron, Andrew J.
Clulow, Ravi C. R. Nagiri, Alpeshkumar K. Malde, Paul L. Burn,* Ian R.
Gentle, Alan E. Mark,* and Benjamin J. Powell
https://doi.org/10.1002/anie.201610727
in the supporting documents page 9 they mentioned how they simulated the
evaporation process.

Regarding the automation and the script writing, I need to insert one
molecule with the required velocity and then remove the atom if moving in
the opposite direction and repeat the process until I have 3000 atom. you
told me to write a script and make each step's output the input to the next
step and so on. how can I do this part linking the step's output to the
next step input.
for example I want:
insert molecule
remove the molecule if moving in the opposite direction
insert
remove if
.
.
.
Do I need just to write it and copy it 3000 time or how can I do it ?

Many Thankss
Mohamed

On Thu, Mar 12, 2020 at 11:51 AM John Whittaker <
johnwhittake at zedat.fu-berlin.de> wrote:

> > 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.
>
> Which paper?
>
> You probably have to add the velocities yourself with a script that
> samples from the Maxwell-Boltzmann distribution at the appropriate
> temperature and adds those velocities to the atoms in your .gro file.
>
> Perhaps there is an easier way that someone can shed some light on, but
> that's what immediately comes to mind.
>
> - John
>
> >
> >
> > 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
> >> >>> --
> >> >>> Gromacs Users mailing list
> >> >>>
> >> >>> * Please search the archive at
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> >> >>> posting!
> >> >>>
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> >> or
> >> >> send
> >> >>> a mail to gmx-users-request at gromacs.org.
> >> >>>
> >> >>
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
> >> >> * Please search the archive at
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> >> >> posting!
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> or
> >> >> send a mail to gmx-users-request at gromacs.org.
> >> >>
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> >>
> > --
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> >
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> >
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>
> --
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>
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