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 <
johnwhitt...@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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