[gmx-users] GROMACS automation

[Justin Lemkul]

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.
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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