[gmx-users] GROMACS automation

Thu Mar 12 14:32:47 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.

Well, for example, you would insert a molecule using gmx insert-molecule
and specify the output file with the -o flag (we'll call the file
conf1.gro)

then, use gmx insert-molecule with conf1.gro as the input and specify the
output file as conf2.gro, and so on...

> for example I want:
> insert molecule
> remove the molecule if moving in the opposite direction

There's no need to remove the molecule. The supporting information you
mentioned says that the z-direction velocities were taken to be the
absolute value, which gets rid of the problem of molecules traveling in
the wrong direction (if the +z direction is where you want the molecules
to travel towards).

> insert
> remove if
> .
> .
> .
> Do I need just to write it and copy it 3000 time or how can I do it ?

Definitely do not copy it 3000 times. Use a simple for loop:

https://www.cyberciti.biz/faq/bash-for-loop/

On the other hand, maybe you should contact the corresponding author of
the paper you linked and ask if they have any advice or leftover scripts
they used to set up the system. It will probably save you some time,
although you won't necessarily learn something new.

Best,

- John

>
> 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
>> >> >>>
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>> >> >>
>> >> >> --
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>> >>
>> >> --
>> >> ==================================================
>> >>
>> >> 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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