No, I use the generate velocity option in the .mdp files. However I want now to assign different velocities in the x,y,z directions. Which I thought it could only be done through the .gro file, but I don't know If I did that, should I change the value of the generate velocity to be = NO in the .mdp files ? (otherwise I would have generated the velocities twice).
Moreover, if I added the velocities in the .gro file how can I generate the velocities in the .gro file from a distribution (Maxwell) with a specific mean and standard deviation ? I have tried to search in different sources (the user list, manual, user guide, research gate and other platforms) how to solve this velocity problem but I didn't find a clear way to insert different velocities in the x,y,z directions using distribution rater than constant velocities. Please guide me how to do it as I am a little bit confused in the velocity generation mechanisms. Many thanks, Mohamed On Mon, Apr 6, 2020 at 6:19 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/6/20 12:16 PM, Mohamed Abdelaal wrote: > > Hello everybody :) > > > > Can I use the gmx insert-molecules to insert molecules in my box with > > velocities by adding the velocities in the .gro file and insert the > > molecules from this .gro file ? > > Have you tried it? > > -Justin > > -- > ================================================== > > 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.