Many thanks Dr. Erik for your reply :)
On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll <ericsm...@gmail.com> wrote: > No problem. > > Now it is clear what you are trying to do. The previous description of > your goals did not make much physical sense. The initial velocities are > such that all three dimensions are sampled from the same 3D velocity > distribution (gaussian with the same width). The difference is that there > is a constant velocity added in the z-direction so there is net motion in > the z-direction. > One way to do this is to use gen-vel as usual and just add the constant to > the z-coordinate. > *Can you please tell me more details how to add the constant to the z-coordinate ? If I will generate the velocity from the .mdp file, in which file should I add the constant to the z-coordinate ? * > The velocities were probably read in. By default, the velocities may not > be printed in the gro. What matters is that they were loaded in the tpr. > Try a simulation to see if the molecule is moving as expected. > I will complete the simulation to the end to check whether or not the velocity was added from my .gro file. > Alternatively, dump the contents of the tpr and make sure the velocities > you created were read in. > > Do you mean that I should manually edit the .tpr file ? I have tried to open it with text editor but it can't be open. > -Eric > > On Tue, Apr 14, 2020 at 1:56 PM Mohamed Abdelaal <m.b.abdel...@gmail.com> > wrote: > > > Sorry for writing again in the same topic but I couldn't solve > > the velocity problem. > > > > I am trying to reproduce a paper written by: Claire Tonnel + , Martin > > Stroet + , Bertrand Caron, Andrew J. Clulow, Ravi C. R. Nagiri, > Alpeshkumar > > K. Malde, Paul L. Burn,* Ian R. Gentle, Alan E. Mark,* and Benjamin J. > > Powell > > Title: Elucidating the Spatial Arrangement of Emitter Molecules in > Organic > > Light-Emitting Diode Films > > > > It was mentioned in the paper that " The molecule was inserted into the > > system such that the x and y coordinates of the centre of mass were > sampled > > from a uniform distribution covering the entire box while the z > coordinate > > of the centre of mass was set to 2.0 nm above the current surface. The > > initial orientation of the molecule was randomised. *The velocities of > each > > atom within the inserted molecule in x and y were sampled from a Gaussian > > distribution with a mean of 0.0 nm/ps and a standard deviation > appropriate > > for the temperature constant (σ = sqrt(kT/m), where k B is Botzmann’s , T > > is the temperature and m is the mass of the atom). The velocities in z > were > > sampled from the distribution with the same standard deviation as x and y > > but with a mean of 0.05 nmps -1 , negative z velocities (molecule moving > in > > the direction opposite to the surface) were rectified by taking the > > absolute value. This ensured all molecules moved toward the surface.* > > > > I have read the section 3.4.1 of the manual version 5.1.2 as recommended > > above and I have also read all the velocity related topics in the manual > > and user guide. > > > > (After Dr. Justin and Dr. Eric replies) I added velocity in my .gro file > > and then I inserted the molecule in a box using insert-molecules, However > > after the insertion process is completed I opened the output .gro file > but > > the velocity was not read. This means that I can only generate the > velocity > > through the .mdp file. > > > > If I am going to generate the velocity using my .mdp file, is it possible > > to change the standard deviation and the mean ? if yes, how can I modify > > them ? (I can't find any way to modify the parameters of the Maxwell > > distribution) > > > > I want to have velocity distributions with means equal to 0,0,0.5 nmps in > > the x,y,z directions respectively. > > > > You wrote in your last email that, "A 3D Maxwell Boltzmann velocity > > distribution corresponds to three identical gaussian speed distributions > in > > vx, vy, andvz 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." > > > > If the velocity will not be read from the .gro file where should I add > the > > constant to change the mean? > > > > Many thanks, > > Mohamed > > > > > > On Thu, Apr 9, 2020 at 5:00 AM Mohamed Abdelaal <m.b.abdel...@gmail.com> > > wrote: > > > > > 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? 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