[gmx-users] GROMACS automation

[John Whittaker]

> 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
>> >>> --
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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.
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>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
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