My knowledge is a bit old. Tpr files are binary so you cannot read them without a special tool. In gromacs 2018, there was a tool that would spit out the contents of a tpr file in a readable format. Execute “gmx dump -h” to learn more.
Justin is correct. There is no tool or file that will allow you to add a constant velocity in the z direction to a set of atoms. I would suggest writing a program to build a custom gro file from the start that has everything you want. If that is not possible for you, you could use gen-vel and attempt to export a gro with the resulting velocities at some point afterward (e.g., use gen-vel tpr for a 1 step simulation writing coordinates and velocities to the trr at every step and then extract gro with velocities from the trr). Then go through the gro file and add a constant z-velocity to all the atoms that need it. Then read the edited gro file in again and proceed. -Eric Sent from my iPhone > On Apr 14, 2020, at 3:02 PM, Mohamed Abdelaal <m.b.abdel...@gmail.com> wrote: > > 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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