Many thanks for your reply :) All your language assumptions are true and that is exactly what I wanted to communicate, next time I will try to be more precise and sorry for the confusion 😊
I will read section 3.4.1 again carefully. Thanks again and sorry for the inconvenience. Mohamed On Thu, Apr 9, 2020 at 04:33 Eric Smoll <ericsm...@gmail.com> wrote: > On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal <m.b.abdel...@gmail.com> > wrote: > > > 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. > > > > I think you mean "same velocity *distributions* in the x, y, and z > directions." The distributions will be approximately the same but each > atom will have a different velocity. > > > > > 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). > > > > I think you mean "specify different velocity *distributions* in the x, y, > and z directions" > > > > > Is it possible to generate different velocities in the x,y and z > directions > > > > I think you mean "generate different velocity *distributions* in the x, y, > and z directions." If so, the answer is obviously yes. Because you can > type in each individual vxi, vyi, and vzi for every atom i, you can > generate different velocity distributions in the x, y, and z directions. > > > > from a maxwell distribution ? > > > I am not sure what this part of the sentence means. If you do what you are > suggesting, you will not be working with a maxwell distribution because all > three directions should have identical distributions. See comment below. > If there is another misunderstanding, you need to spend more time crafting > precise sentences to communicate what you are after. > > > > (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?) > > > > In my last email I suggested reading section 3.4.1 of the manual version > 5.1.2. It seems you did not. A 3D Maxwell Boltzmann velocity distribution > corresponds to three identical gaussian speed distributions in vx, vy, and > vz centered at zero (mean should be zero for vx, vy, vz). Just change the > standard deviation of the velocity distribution sqrt(kT/m) for each > velocity component if you want them to be different. If you don't want the > mean to be zero for whatever reason, add a constant. However, a non-zero > mean for any of the velocity components will generate center of mass > motion. If you want center of mass motion, turn off center of mass motion > removal in the mdp file. > > > > 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 t > <https://www.google.com/maps/search/velocities+by+adding+the+velocities+in+t?entry=gmail&source=g>he > .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. > -- > 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.