Sent from my iPhone
> On Apr 16, 2020, at 7:53 PM, Mohamed Abdelaal <m.b.abdel...@gmail.com> wrote: > > I have one more question please regarding the velocity. No problem. > > What is the mean value for the velocity being generated by GROMACS ? Is it > zero ? Yes. > > 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? Yes you are missing something. Read again. Each random number is generated between 0 and 1 but 12 of these are added together before subtracting 6 from the sum. If, by chance, all twelve numbers are 0.1, the sum is 1.2. 1.2 - 6 is -4.8. This is why negative numbers are possible. > > "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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