Many thanks for your reply 😊 The limitation in the generate velocity using the .mdp file, is that while I can generate the velocity from Maxwell distribution, I will have the same velocities in the x, y and z directions.
On the other hand, generating the velocity from the .gro file will let me specify different velocities in the x,y and z directions but they will be the same velocities for all the atoms (will not be taken from a maxwell distribution with variation in the atoms velocities). Is it possible to generate different velocities in the x,y and z directions from a maxwell distribution ? (for example the velocities to be taken from a maxwell distribution with a mean of 0.1 in the x direction and with a mean of 0.2 in the y direction and with mean of 0.3 in the z direction?) Thanks for your help :) Mohamed On Wed, Apr 8, 2020 at 05:48 Eric Smoll <ericsm...@gmail.com> wrote: > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal <m.b.abdel...@gmail.com> > wrote: > > > 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). > > > > That sounds logical. Set it to no if you provide your own initial > velocities. > > > > > 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. > > > > There is a good section on this in the manual. For example, section > 3.4.1 > in the Gromacs 5.1.2 manual. > > Also, you know that the generate velocities option assigns velocities to > atoms from an approximate MB distribution at whatever temperature you > specify in the MDP file, right? If I understand you correctly, the > generate velocities options should do exactly what you want. With no extra > work. > > > > 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. > > > -- > 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.