I have one more question please regarding the velocity. What is the mean value for the velocity being generated by GROMACS ? Is it zero ?
I have also understood fr om the below paragraph which is written in the manual section 3.4.1, that the values generated are selected from the range between 0 and 1, However I have opened my nvt.gro file and I have found negative values for the generated velocity. How come that I have negative values for the velocity if the generated velocity is within the range from 0-1 as written in the manual ? Am I missing something? "If velocities are not available, the program can generate initial atomic velocities at a given absolute temperature T : where k is Boltzmann’s constant (see chapter 2). To accomplish this, normally distributed random numbers are generated by adding twelve random numbers R k in the range 0 ≤ R k < 1 and subtracting 6.0 from their sum. The result is then multiplied by the standard deviation of the velocity distribution kT /m i . Since the resulting total energy will not correspond exactly to the required temperature T , a correction is made: first the center-of-mass motion is removed and then all velocities are scaled so that the total energy corresponds exactly to T (see eqn. 3.18)." Many thanks, Mohamed On Wed, Apr 15, 2020 at 12:26 AM Eric Smoll <ericsm...@gmail.com> wrote: > 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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