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.
On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul <jalem...@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 < > > 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 > >>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at > >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >>> posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send > >>> a mail to gmx-users-requ...@gromacs.org. > >>> > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.