Re: [gmx-users] Velocities from the .gro file
Sent from my iPhone > On Apr 16, 2020, at 7:53 PM, Mohamed Abdelaal 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 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 >> wrote: >>> >>> Many thanks Dr. Erik for your reply :) >>> >>> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll >> 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
Re: [gmx-users] Velocities from the .gro file
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 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 > wrote: > > > > Many thanks Dr. Erik for your reply :) > > > > > >> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll > 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 > >>>
Re: [gmx-users] Velocities from the .gro file
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 wrote: > > Many thanks Dr. Erik for your reply :) > > >> On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll 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 >> 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
Re: [gmx-users] Velocities from the .gro file
Many thanks Dr. Erik for your reply :) On Tue, Apr 14, 2020 at 11:15 PM Eric Smoll 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 > 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 > > 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 wrote: > > > > > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal < >
Re: [gmx-users] Velocities from the .gro file
Many thanks for your quick reply :) On Tue, Apr 14, 2020 at 11:09 PM Justin Lemkul wrote: > > > On 4/14/20 4:55 PM, Mohamed Abdelaal 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.* > > Presumably the authors used different software; GROMACS does not allow > such granular control of velocities. > > > 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. > > That's not true. If you know what velocities you want to assign, do so > *after* building the whole system by writing the velocities to the .gro > file (you will need your own code/script to do this). Then do not > generate velocities in the .mdp file and they will be read from the .gro > 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) > > No, GROMACS has no such capability. > > -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.
Re: [gmx-users] Velocities from the .gro file
On 4/14/20 4:55 PM, Mohamed Abdelaal 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.* Presumably the authors used different software; GROMACS does not allow such granular control of velocities. 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. That's not true. If you know what velocities you want to assign, do so *after* building the whole system by writing the velocities to the .gro file (you will need your own code/script to do this). Then do not generate velocities in the .mdp file and they will be read from the .gro 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) No, GROMACS has no such capability. -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.
Re: [gmx-users] Velocities from the .gro file
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 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 wrote: > >> On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal >> 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
Re: [gmx-users] Velocities from the .gro file
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 wrote: > On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal > 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 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 > wrote: > > > > > > > > > > >
Re: [gmx-users] Velocities from the .gro file
On Wed, Apr 8, 2020 at 4:41 PM Mohamed Abdelaal 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 wrote: > > > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal > > 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 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 the .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
Re: [gmx-users] Velocities from the .gro file
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. 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). Is it possible to generate different velocities in the x,y and z directions from a maxwell distribution ? (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?) Thanks for your help :) Mohamed On Wed, Apr 8, 2020 at 05:48 Eric Smoll wrote: > On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal > 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 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 the .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.
Re: [gmx-users] Velocities from the .gro file
On Tue, Apr 7, 2020 at 3:38 PM Mohamed Abdelaal 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 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 the .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.
Re: [gmx-users] Velocities from the .gro file
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). 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. 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 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 the .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.
Re: [gmx-users] Velocities from the .gro file
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 the .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.
