Re: [gmx-users] Lincs warning and Bond length not finite
Many thanks Alex for your reply :) You have pressure scaling and LINCS convergence issues, suggesting that > the starting configuration is far from equilibrium, as well as > potentially other issues. > > How to check if my starting configuration is far from equilibrium ? I checked the Temperature and Pressure curves ( attached in the original email) and they look equilibirated. Is there anything I am missing? > Gromos FF is not appropriate for graphene, and neither is turning C-C > bonds into LINCS constraints, as set by your 'all-bonds' -- graphene is > not a small organic molecule or a protein. Also, if your system is > periodic in all directions, make sure the graphene edges are > crystallographically commensurate with respect to PBC and the box size > is appropriate. How can I make that my graphene edges are crystallographically commensurate with respect to PBC ? I have chosen box size equal to the graphene sheet size and increased the height to make sure that the deposited molecules will not be deposited out of my graphene sheet area. > Finally, make sure that the small molecules you're > depositing on graphene are properly pre-equilibrated. > > Actually, after your email, I did the simulation for both the graphene sheet and the deposited molecules (C60) each alone to check with one has problems with the lincs warning. The C60 alone was successfully completed. The Graphene sheet didn't work due to the lincs warning. I know now that the problem is only in the graphene sheet. > Alex > > Thanks, Mohamed > On 5/3/2020 6:39 PM, Mohamed Abdelaal wrote: > > Hello everyone, > > > > I am simulating the evaporation of non protein molecules on a graphene > > sheet. I am using gromos force field and hence the lincs constrain are > set > > to all-bonds. I have done the energy minimization and NVT > > successfully without any warnings. During the NPT equilibiration I got > > Lincs warning but the NPT equilibiration was completed to the end. During > > the md production run, I received lincs warning and Bond length not > finite > > and sometimes I received " nonbonded interaction between particles is > > larger than the table limit 2.437 nm". > > > > I have read that this means that my system is blowing up. Hence, I have > > read the Blowing up and diagnosing unstable system on gromacs website, I > > can't recognize any of the posted issues in my files/simulation and > > hence, I can't decide what exactly is the problem or what should I > change > > (it seems that my system is well minimized and the temperature and > pressure > > looks fine). I have added in the below link, the NPT and md logs and > .mdp > > files and pictures for the potential energy, Temperature, Pressure and > > Density. > > > > https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF > > > > I have tried the simulation again with none as lincs constrains and it > > worked without any errors. > > > > I think the problem has something to do with the pressure since the > problem > > started during the NPT, but I don't know how exactly to find the problem. > > Can anyone guide me please what should I change or how should I start ? > > > > Thanks, > > Mohamed > -- > 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] Free volume variation during the simulation
Many thanks david for the explanation. In did NVT then NPT equilibiration and then the production run, in the production run .mdp file I have the same parameters as in NVT and NPT.mdp files. Does this mean that my simulation is a NVT simulation or NPT ? Is it possible to do only one of them (NVT or NPT) equilibiration ? I thought that I must do both of them before I start the final production run. Thanks again, Mohamed On Wed, May 6, 2020 at 12:50 PM David van der Spoel wrote: > Den 2020-05-06 kl. 10:21, skrev Mohamed Abdelaal: > > Yes I measured both, the density and the free volume using gromacs. > > > > Since the free volume changes with respect to time, shouldn’t the density > > also change with time ? > What do you mean with "changes"? If the density is constant (with > fluctuations) in an equilibrium NPT simulation then the free volume > should fluctuate around an average as well. > > If you have a NVT simulation on the other hand, the total density is > going to be constant, but if your system undergoes a phase change the > freevolume will change. > > > > Thanks, > > Mohamed > > > > On Wed, May 6, 2020 at 08:23 David van der Spoel > > wrote: > > > >> Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > >>> Hello everybody, > >>> > >>> I have two fundamental questions please. > >>> > >>> I have measured the fee volume and I discovered that, the free volume > >>> changes with respect to the time during the production run (different > >> value > >>> for each frame). However I have measured the density but the result > does > >>> not change with respect to time. > >>> > >>> Shouldn't the density also changes with time if the free volume changes > >>> with time ? > >>> > >>> I also can't understand why the free volume changes with respect to the > >>> time, if the number of molecules and volume of box didn't change. > >>> > >>> Many Thanks, > >>> Mohamed > >>> > >> This is due to atomic fluctuations, that is they overlap more or less > >> depending on their distance, Did you use the freevolume tool in gromacs? > >> It may also depend on whether each freevolume calculations is converged > >> (-ninsert option). > >> > >> -- > >> David van der Spoel, Ph.D., > >> Professor of Biology > >> Uppsala University. > >> http://virtualchemistry.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. > >> > > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.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] Free volume variation during the simulation
I started with NVT then NPT then md production run. Thanks, Kohamed On Wed, May 6, 2020 at 10:40 Arun Srikanth wrote: > Is it an NPT simulation or NVT simulation? > Arun > > On Wed, 6 May 2020, 9:27 am Mohamed Abdelaal, > wrote: > > > Yes I measured both, the density and the free volume using gromacs. > > > > Since the free volume changes with respect to time, shouldn’t the density > > also change with time ? > > > > Thanks, > > Mohamed > > > > On Wed, May 6, 2020 at 08:23 David van der Spoel > > wrote: > > > > > Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > > > > Hello everybody, > > > > > > > > I have two fundamental questions please. > > > > > > > > I have measured the fee volume and I discovered that, the free volume > > > > changes with respect to the time during the production run (different > > > value > > > > for each frame). However I have measured the density but the result > > does > > > > not change with respect to time. > > > > > > > > Shouldn't the density also changes with time if the free volume > changes > > > > with time ? > > > > > > > > I also can't understand why the free volume changes with respect to > the > > > > time, if the number of molecules and volume of box didn't change. > > > > > > > > Many Thanks, > > > > Mohamed > > > > > > > This is due to atomic fluctuations, that is they overlap more or less > > > depending on their distance, Did you use the freevolume tool in > gromacs? > > > It may also depend on whether each freevolume calculations is converged > > > (-ninsert option). > > > > > > -- > > > David van der Spoel, Ph.D., > > > Professor of Biology > > > Uppsala University. > > > http://virtualchemistry.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. -- 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] Free volume variation during the simulation
Yes I measured both, the density and the free volume using gromacs. Since the free volume changes with respect to time, shouldn’t the density also change with time ? Thanks, Mohamed On Wed, May 6, 2020 at 08:23 David van der Spoel wrote: > Den 2020-05-06 kl. 01:13, skrev Mohamed Abdelaal: > > Hello everybody, > > > > I have two fundamental questions please. > > > > I have measured the fee volume and I discovered that, the free volume > > changes with respect to the time during the production run (different > value > > for each frame). However I have measured the density but the result does > > not change with respect to time. > > > > Shouldn't the density also changes with time if the free volume changes > > with time ? > > > > I also can't understand why the free volume changes with respect to the > > time, if the number of molecules and volume of box didn't change. > > > > Many Thanks, > > Mohamed > > > This is due to atomic fluctuations, that is they overlap more or less > depending on their distance, Did you use the freevolume tool in gromacs? > It may also depend on whether each freevolume calculations is converged > (-ninsert option). > > -- > David van der Spoel, Ph.D., > Professor of Biology > Uppsala University. > http://virtualchemistry.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] Free volume variation during the simulation
I am simulating Crystal System (C60 molecules) Thanks, Mohamed On Wed, May 6, 2020 at 1:22 AM Arun Srikanth wrote: > Are you simulating a crystal or amorphous system? > > Arun > > On Wed, May 6, 2020 at 12:13 AM Mohamed Abdelaal > wrote: > > > Hello everybody, > > > > I have two fundamental questions please. > > > > I have measured the fee volume and I discovered that, the free volume > > changes with respect to the time during the production run (different > value > > for each frame). However I have measured the density but the result does > > not change with respect to time. > > > > Shouldn't the density also changes with time if the free volume changes > > with time ? > > > > I also can't understand why the free volume changes with respect to the > > time, if the number of molecules and volume of box didn't change. > > > > Many Thanks, > > Mohamed > > -- > > 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.
[gmx-users] Free volume variation during the simulation
Hello everybody, I have two fundamental questions please. I have measured the fee volume and I discovered that, the free volume changes with respect to the time during the production run (different value for each frame). However I have measured the density but the result does not change with respect to time. Shouldn't the density also changes with time if the free volume changes with time ? I also can't understand why the free volume changes with respect to the time, if the number of molecules and volume of box didn't change. Many Thanks, Mohamed -- 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.
[gmx-users] Lincs warning and Bond length not finite
Hello everyone, I am simulating the evaporation of non protein molecules on a graphene sheet. I am using gromos force field and hence the lincs constrain are set to all-bonds. I have done the energy minimization and NVT successfully without any warnings. During the NPT equilibiration I got Lincs warning but the NPT equilibiration was completed to the end. During the md production run, I received lincs warning and Bond length not finite and sometimes I received " nonbonded interaction between particles is larger than the table limit 2.437 nm". I have read that this means that my system is blowing up. Hence, I have read the Blowing up and diagnosing unstable system on gromacs website, I can't recognize any of the posted issues in my files/simulation and hence, I can't decide what exactly is the problem or what should I change (it seems that my system is well minimized and the temperature and pressure looks fine). I have added in the below link, the NPT and md logs and .mdp files and pictures for the potential energy, Temperature, Pressure and Density. https://drive.google.com/drive/folders/1yyUJNg4yXnPfsxZ9gQ4LV5sqRKnJq9rF I have tried the simulation again with none as lincs constrains and it worked without any errors. I think the problem has something to do with the pressure since the problem started during the NPT, but I don't know how exactly to find the problem. Can anyone guide me please what should I change or how should I start ? Thanks, Mohamed -- 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.
[gmx-users] PBC after energy minimization
Hello everybody, In order to solve the PBC at the end I use the command: *gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_noPBC.xtc -pbc mol * followed by: *gmx trjconv -s md_0_1.tpr -f md_noPBC.xtc -o md_noPBC.pdb* I want to solve this problem after the energy minimization but I don't have .xtc file to use it as I do at the end. How can I solve this problem after the energy minimization ? Thanks, Mohamed -- 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.
[gmx-users] Periodic boundary conditions during the simulation
Hello everybody, I know that due to periodic boundary conditions the molecules move from one side of the box to the other side and moves outside the box. I also know how to use trjconv to solve this problem and I usually do this step at the end of the simulation. However I have noticed that after the energy minimization, some molecules which were position restrained at the bottom of the box have been moved to the top of the box. I knew that I have this periodic boundary condition problem not just from visualization of the structure after the energy minimization, but also from the atoms coordinates in the .gro file after the energy minimization, the z coordinate of some atoms have been changed from bottom to top as below: before energy minimization: (the z coordinate was always zero) 1GRM C11 0.061 0.071 0.000 1GRM C22 0.184 0.142 0.000 1GRM C33 0.184 0.284 0.000 1GRM C44 0.061 0.355 0.000 2GRM C15 0.061 0.497 0.000 after energy minimization: (z coordinate of some atoms have been changed into 14 which is at the top of the box) 1GRM C11 0.061 0.071 14.000 1GRM C22 0.184 0.142 14.000 1GRM C33 0.184 0.284 0.000 1GRM C44 0.061 0.355 0.000 2GRM C15 0.061 0.497 14.000 Do I need to solve this PBC problem between the different steps (energy min, NVT, NPT, production run) or it is okay to continue my simulation (even if the molecules have moved) and solve this problem at the end ? Many thanks, Mohamed -- 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.
[gmx-users] Does the energy minimization deals with velocity ?
Hello everyone, If I will add the velocity manually to my system, should I add them before the energy minimization or after ? I will do the below steps: 1. insert molecules 2. energy minimization 3. NVT equilibiration 4. NPT equilibiration 5. production run. should I add the velocity before the NVT equilibiration step or before the energy minimization ? I am trying to reproduce the results of the below paper: Title: Morphology of a Bulk Heterojunction Photovoltaic Cell with Low Donor Concentration Authors: Thomas Lee, † Audrey Sanzogni, † Ningxin Zhangzhou, † Paul L. Burn,* ,†,‡ and Alan E. Mark* ,† Paragraph: All deposition simulations were performed using the GROMACS simulation package version 4.6. 27. During the deposition process, new molecules were inserted 2 nm from the top of the film every 10 ps with a random orientation and an initial velocity toward the surface to ensure they reach the growing film. The net velocity was randomly selected from a normal distribution with a mean of 0.05 nm ps −1 and a standard deviation of square root ( k B T / m) where m is the mass of the molecule. Molecules that were more than 1 nm above the top of the film and moving away from the substrate (after having bounced on impact or sublimed from the surface) *were removed prior to the insertion of the next molecule.* The highlighted paragraph means that each inserted molecule had the time to move until it reaches the growing film before inserting the next molecule. I thought I can do that by doing energy minimization between single molecules insertion. But if the molecules will not move during the energy minimization then how can I allow each molecule to move to the growing molecule before inserting the next molecule ? Thanks, Mohamed -- 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
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 Spatia
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: > > > >
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
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
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 t
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
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.
[gmx-users] Velocities from the .gro file
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 ? Thanks Mohamed -- 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.
[gmx-users] Generating velocities
Hello everybody, If my molecules are moving and I want to add the velocity, should I generate the velocity through the .mdp file, or should I add the velocities into my .gro file and insert the molecules? Thanks, Mohamed -- 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.
[gmx-users] Temperature and Pressure coupling in NVT.mdp, NPT.mdp and md.mdp
Hello everybody, Can anybody please help me as I am confused between the Temperature and Pressure coupling in the different .mdp files. Can you please tell me what is the difference between the Temperature and Pressure coupling in the NVT.mdp, NPT.mdp during the equilibration and in the md.mdp during the production run? In my project I am simulating the vacuum evaporation, So, I am inserting molecules in the vacuum and they should be at high temperatures (evaporation temperature) and at vacuum pressure. Should I add these 2 conditions through temperature and pressure coupling in the NVT.mdp and NPT.mdp during equilibration and also in the md.mdp during the production run? If yes, is there any difference between the NVT.mdp, NPT.mdp and the md.mdp in terms of temperature and pressure coupling ? If my molecules are moving with a specific velocity, should I generate the velocity in the NVT.mdp, NPT.mdp and in the md.mdp ? Many Thanks, Mohamed -- 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] GROMACS automation
The paper information is as below : Title: Elucidating the Spatial Arrangement of Emitter Molecules in Organic Light-Emitting Diode Films Authors: 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 https://doi.org/10.1002/anie.201610727 in the supporting documents page 9 they mentioned how they simulated the evaporation process. Regarding the automation and the script writing, I need to insert one molecule with the required velocity and then remove the atom if moving in the opposite direction and repeat the process until I have 3000 atom. you told me to write a script and make each step's output the input to the next step and so on. how can I do this part linking the step's output to the next step input. for example I want: insert molecule remove the molecule if moving in the opposite direction insert remove if . . . Do I need just to write it and copy it 3000 time or how can I do it ? Many Thankss Mohamed On Thu, Mar 12, 2020 at 11:51 AM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > > I was planning to put the velocities in the .gro file from which I am > > inserting the molecules. If the gmx insert-molecules will ignore the > > velocities of the atoms, can you please guide me how can I insert the > > molecules with a velocity ? > > I have read a paper which mentions that they inserted the molecules and > > the velocities of the ATOMS were sampled from a distribution with > standard > > deviation =xx and mean = xxx. > > Which paper? > > You probably have to add the velocities yourself with a script that > samples from the Maxwell-Boltzmann distribution at the appropriate > temperature and adds those velocities to the atoms in your .gro file. > > Perhaps there is an easier way that someone can shed some light on, but > that's what immediately comes to mind. > > - John > > > > > > > On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: > > > >> > >> > >> On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: > >> > I want to insert an atom with a velocity moving downwards toward the > >> > graphene sheet in my box. > >> > Yes I need to remove any atom moving away from my substrate or the > >> > deposited atoms and far by 0.4 nm. > >> > Then repeat the process until I have inserted 3000 atoms. > >> > >> gmx insert-molecules has no knowledge of velocities, and atoms are not > >> inserted with any velocity, only a position. > >> > >> Removal of atoms is handled with gmx trjconv and a suitable index file > >> generated by gmx select (in this case, since you're specifying a > >> geometric criterion). > >> > >> -Justin > >> > >> > Thanks for your reply. > >> > Mohamed > >> > > >> > On Wed, Mar 11, 2020 at 13:43 John Whittaker < > >> > johnwhitt...@zedat.fu-berlin.de> wrote: > >> > > >> >> Write a script that calls gmx insert-molecules 3000 times and uses > >> the > >> >> previous output as input for each call. > >> >> > >> >> > >> >> > >> > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > >> >> > >> >> Is there something you have to do in between each insertion? > >> >> > >> >> - John > >> >> > >> >>> Hello everybody, > >> >>> > >> >>> I am trying to insert molecules into a box but I have to insert one > >> >> single > >> >>> molecule at a time reaching 3000 molecule in total. Is there a way > >> to > >> >>> automate this process ? > >> >>> > >> >>> Thanks > >> >>> Mohamed > >> >>> -- > >> >>> 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] GROMACS automation
I was planning to put the velocities in the .gro file from which I am inserting the molecules. If the gmx insert-molecules will ignore the velocities of the atoms, can you please guide me how can I insert the molecules with a velocity ? I have read a paper which mentions that they inserted the molecules and the velocities of the ATOMS were sampled from a distribution with standard deviation =xx and mean = xxx. On Wed, Mar 11, 2020 at 7:05 PM Justin Lemkul wrote: > > > On 3/11/20 9:56 AM, Mohamed Abdelaal wrote: > > I want to insert an atom with a velocity moving downwards toward the > > graphene sheet in my box. > > Yes I need to remove any atom moving away from my substrate or the > > deposited atoms and far by 0.4 nm. > > Then repeat the process until I have inserted 3000 atoms. > > gmx insert-molecules has no knowledge of velocities, and atoms are not > inserted with any velocity, only a position. > > Removal of atoms is handled with gmx trjconv and a suitable index file > generated by gmx select (in this case, since you're specifying a > geometric criterion). > > -Justin > > > Thanks for your reply. > > Mohamed > > > > On Wed, Mar 11, 2020 at 13:43 John Whittaker < > > johnwhitt...@zedat.fu-berlin.de> wrote: > > > >> Write a script that calls gmx insert-molecules 3000 times and uses the > >> previous output as input for each call. > >> > >> > >> > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > >> > >> Is there something you have to do in between each insertion? > >> > >> - John > >> > >>> Hello everybody, > >>> > >>> I am trying to insert molecules into a box but I have to insert one > >> single > >>> molecule at a time reaching 3000 molecule in total. Is there a way to > >>> automate this process ? > >>> > >>> Thanks > >>> Mohamed > >>> -- > >>> 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. > >> > > -- > == > > 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] GROMACS automation
I want to insert an atom with a velocity moving downwards toward the graphene sheet in my box. Yes I need to remove any atom moving away from my substrate or the deposited atoms and far by 0.4 nm. Then repeat the process until I have inserted 3000 atoms. Thanks for your reply. Mohamed On Wed, Mar 11, 2020 at 13:43 John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > Write a script that calls gmx insert-molecules 3000 times and uses the > previous output as input for each call. > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-insert-molecules.html > > Is there something you have to do in between each insertion? > > - John > > > Hello everybody, > > > > I am trying to insert molecules into a box but I have to insert one > single > > molecule at a time reaching 3000 molecule in total. Is there a way to > > automate this process ? > > > > Thanks > > Mohamed > > -- > > 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.
[gmx-users] GROMACS automation
Hello everybody, I am trying to insert molecules into a box but I have to insert one single molecule at a time reaching 3000 molecule in total. Is there a way to automate this process ? Thanks Mohamed -- 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.
[gmx-users] core dump
Hello everybody I have been using GROMACS 2018.1 in the last month and I got an error "core dumped" while running the simulation. Accordingly, I have installed the 2020.1 version and while I am doing pressure equilibration (npt), I had the same error again (I paste it below) which is core dumped. Is it a problem in this version or I might have done something wrong while running the equilibration ? I would really appreciate it, if anyone can guide me. I have pasted the error below Thanks Mohamed :-) GROMACS - gmx mdrun, 2020.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca HamuraruVincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. LemkulViveca LindahlMagnus Lundborg Erik Marklund Pascal Merz Pieter MeulenhoffTeemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael ShirtsAlexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian WennbergMaarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2020.1 Executable: /home/abdelaal/build2/gromacs-2020.1/build/bin/gmx Data prefix: /home/abdelaal/build2/gromacs-2020.1 (source tree) Working dir: /home/abdelaal/Desktop/GROMACS/C60:TAPC/C60_GRM/22 Command line: gmx mdrun -v -deffnm npt Reading file npt.tpr, VERSION 2020.1 (single precision) Changing nstlist from 10 to 100, rlist from 1 to 1 Using 1 MPI thread Non-default thread affinity set, disabling internal thread affinity Using 8 OpenMP threads starting mdrun 'GRM in vacuum' 5 steps, 25.0 ps. step 44700, remaining wall clock time: 137 s Step 44790 Warning: pressure scaling more than 1%, mu: 1.01937 1.01937 1.01937 Segmentation fault (core dumped) -- 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.
[gmx-users] Collision
Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I should restrain the graphene sheet along the z axis. I did that using force =1000. and the problem was solved and nothing moved. After that I tried to insert 25 molecule of (C60) inside a box which contains the graphene sheet. I did that and did the energy minimization but part of the graphene sheet moved again from its place although the maximum force was less than 1000 which is the force I used to restrain the graphene sheet. However I didn't have any error during the energy minimization. Does this means that the problem is just in visualization or I might have a problem in my energy minimization ? It is also worth mentioning that the C60 molecules are not spherical as it should be. I read about that and I found people mentioning that this shape deformation in only a visualization problem and can be solved by using gmx trjconv. is it possible that this problem has happened to my whole system including the graphene sheet or it shouldn't affect my graphene sheet as long as I have restrained it ? more info: I used periodic_molecules = yes while trying to minimize my whole system. (I also tried without it but no impact) I wrote: gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p C60_GRM_box.top -o min1.tpr -maxwarn 2 followed by gmx mdrun -v -deffnm min1 and I got the below result: writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 3293 steps Potential Energy = 6.3598562e+05 Maximum force = 9.9486487e+02 on atom 12087 Norm of force = 6.5454323e+01 Can anybody help me please. Thanks Mohamed -- 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.
[gmx-users] Energy minimization
Hello all, I created a graphene sheet and performed energy minimization, after energy minimization I found that parts of the graphene sheet was moved from the box bottom to the box topside at the same place (as if it was translated upwards). I looked online for the problem and I understood that I should restrain the graphene sheet along the z axis. I did that using force =1000. and the problem was solved and nothing moved. After that I tried to insert 25 molecule of (C60) inside a box which contains the graphene sheet. I did that and did the energy minimization but part of the graphene sheet moved again from its place although the maximum force was less than 1000 which is the force I used to restrain the graphene sheet. However I didn't have any error during the energy minimization. Does this means that the problem is just in visualization or I might have a problem in my energy minimization ? It is also worth mentioning that the C60 molecules are not spherical as it should be. I read about that and I found people mentioning that this shape deformation in only a visualization problem and can be solved by using gmx trjconv. is it possible that this problem has happened to my whole system including the graphene sheet or it shouldn't affect my graphene sheet as long as I have restrained it ? more info: I used periodic_molecules = yes while trying to minimize my whole system. (I also tried without it but no impact) I wrote: gmx grompp -f minim.mdp -c C60_GRM_box.gro -r C60_GRM_box.gro -p C60_GRM_box.top -o min1.tpr -maxwarn 2 followed by gmx mdrun -v -deffnm min1 and I got the below result: writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 3293 steps Potential Energy = 6.3598562e+05 Maximum force = 9.9486487e+02 on atom 12087 Norm of force = 6.5454323e+01 Can anybody help me please. Thanks Mohamed -- 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] Increase Graphene sheet size
Hi Alessandra, Many thanks again for your help :) That sounds great. I can simulate a box with the desired dimensions. I repeated the graphene sheet using genconf into dimensions greater the desired dimensions and then I created a box with the desired dimensions and I solvate it to visualize it. now I have an additional part of the graphene sheet which is out of the box, How can I remove it. I want my simulation and visualization to be with a specific dimensions which is the dimensions of the box. I would appreciate if you can further clarify how can I do that. Thanks, Mohamed On Wed, Feb 19, 2020 at 10:10 Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > HI, > > > > On Wed, Feb 19, 2020 at 10:31 AM Mohamed Abdelaal > wrote: > > > Many thanks Alessandra for your reply :) > > > > gmx solvate will add water around my graphene sheet but will not increase > > the graphene sheet itself. Please correct me if I am wrong. > > > > > Yes/No, gmx solvate is normally used to add water or to build solvent box > but my suggestion was to use gmx solvate tools for your aim. > What I suggested was to use the tool to fill an empty box (of desidered > dimension) with copies of your graphene pre-equilibrated (small) sheet. > > Best regards > Alessandra > > > > I already simulated the graphene sheet but I need to increase its > dimension > > to a certain dimensions. > > > > any Ideas how to do that :) ? > > > > Thanks, > > Mohamed > > > > On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < > > alessandra.villa.bio...@gmail.com> wrote: > > > > > Hi > > > > > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal < > > m.b.abdel...@gmail.com> > > > wrote: > > > > > > > Hello All, > > > > > > > > I want to create a graphene sheet with a specific dimensions > > > (10*15*0.284) > > > > nm. > > > > > > > > I created a .gro file as below ( as mentioned in this website > > > > > > > > > > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > > > ) > > > > > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > > > 4 > > > > 1GRM C1 1 0.061 0.071 0.000 > > > > 1GRM C2 2 0.184 0.142 0.000 > > > > 1GRM C3 3 0.184 0.284 0.000 > > > > 1GRM C4 4 0.061 0.355 0.000 > > > > 0.2459510.4260000.284000 > > > > > > > > Now I don't know how to use genconf to repeat it until it gives me > the > > > > required dimensions. As using genconf -nbox will repeat the above > into > > a > > > > specific number of boxes but I can't get a sheet with accurate > > dimensions > > > > of (10*15*0.284 nm). > > > > > > > > I tried to generate a sheet using gencong and then use editconf to > > change > > > > the dimensions to the required ones, but the problem is that using > > > editconf > > > > will put the graphene sheet in an empty box but will not change the > > > > dimension as I want. > > > > > > > > Another option is to divide the 10 (the required dimension) nm by > > > 0.245951 > > > > (the dimension in the above .gro file) and to use the genconf with > the > > > > result but it will be a lot of decimals and I am not sure if it will > > also > > > > give me the accurate dimension. > > > > > > > > Can anybody help me or guide me how to solve that problem. > > > > > > > > > > > you could try gmx solvate. It is not elegant solution but it may work, > > the > > > limitation is that you do not control on the orientation and other > > > geometrical parameter that may be relevant for graphene sheet. > > > > > > 1) generate an empty box with the desired dimension (empty.gro) > > > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro . -o > > > > > > or in alternative you can use -cs and -box > > > for all the options see > > > > > > > > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > > > > > Best regards > > > Alessandra > > > > > > > > > > Thanks, > > > > Mohamed > > > > -- > > > > Gro
Re: [gmx-users] Increase Graphene sheet size
Many thanks Alessandra for your reply :) gmx solvate will add water around my graphene sheet but will not increase the graphene sheet itself. Please correct me if I am wrong. I already simulated the graphene sheet but I need to increase its dimension to a certain dimensions. any Ideas how to do that :) ? Thanks, Mohamed On Tue, Feb 18, 2020 at 8:16 AM Alessandra Villa < alessandra.villa.bio...@gmail.com> wrote: > Hi > > On Mon, Feb 17, 2020 at 11:11 AM Mohamed Abdelaal > wrote: > > > Hello All, > > > > I want to create a graphene sheet with a specific dimensions > (10*15*0.284) > > nm. > > > > I created a .gro file as below ( as mentioned in this website > > > > > https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ > > ) > > > > GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring > > 4 > > 1GRM C1 1 0.061 0.071 0.000 > > 1GRM C2 2 0.184 0.142 0.000 > > 1GRM C3 3 0.184 0.284 0.000 > > 1GRM C4 4 0.061 0.355 0.000 > > 0.2459510.4260000.284000 > > > > Now I don't know how to use genconf to repeat it until it gives me the > > required dimensions. As using genconf -nbox will repeat the above into a > > specific number of boxes but I can't get a sheet with accurate dimensions > > of (10*15*0.284 nm). > > > > I tried to generate a sheet using gencong and then use editconf to change > > the dimensions to the required ones, but the problem is that using > editconf > > will put the graphene sheet in an empty box but will not change the > > dimension as I want. > > > > Another option is to divide the 10 (the required dimension) nm by > 0.245951 > > (the dimension in the above .gro file) and to use the genconf with the > > result but it will be a lot of decimals and I am not sure if it will also > > give me the accurate dimension. > > > > Can anybody help me or guide me how to solve that problem. > > > > > you could try gmx solvate. It is not elegant solution but it may work, the > limitation is that you do not control on the orientation and other > geometrical parameter that may be relevant for graphene sheet. > > 1) generate an empty box with the desired dimension (empty.gro) > 2) run gmx solvate -cp empty.gro -cs small_graphene.gro . -o > > or in alternative you can use -cs and -box > for all the options see > > http://manual.gromacs.org/documentation/current/onlinehelp/gmx-solvate.html?highlight=gmx%20solvate > > Best regards > Alessandra > > > > Thanks, > > Mohamed > > -- > > 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.
[gmx-users] Increase Graphene sheet size
Hello All, I want to create a graphene sheet with a specific dimensions (10*15*0.284) nm. I created a .gro file as below ( as mentioned in this website https://erastova.xyz/teaching/practical-simulations-for-molecules-and-materials/material-simulations/graphene-simulation-set-up/ ) GRM: 1 1 Rcc=1.420 Rhole=0.000 Center: Ring 4 1GRM C1 1 0.061 0.071 0.000 1GRM C2 2 0.184 0.142 0.000 1GRM C3 3 0.184 0.284 0.000 1GRM C4 4 0.061 0.355 0.000 0.2459510.4260000.284000 Now I don't know how to use genconf to repeat it until it gives me the required dimensions. As using genconf -nbox will repeat the above into a specific number of boxes but I can't get a sheet with accurate dimensions of (10*15*0.284 nm). I tried to generate a sheet using gencong and then use editconf to change the dimensions to the required ones, but the problem is that using editconf will put the graphene sheet in an empty box but will not change the dimension as I want. Another option is to divide the 10 (the required dimension) nm by 0.245951 (the dimension in the above .gro file) and to use the genconf with the result but it will be a lot of decimals and I am not sure if it will also give me the accurate dimension. Can anybody help me or guide me how to solve that problem. Thanks, Mohamed -- 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] Graphene Sheet in GROMOS 54A7
many thanks for your reply :) I have the graphene sheet topology file .itp not .top. I am trying to evaporate some molecules on the graphene sheet. Unfortunately, I didn't find information in the manual about how to do such an evaporation on the graphene sheet. what I have now is the graphene sheet topology .itp and the topology file .itp for the molecule that I want to evaporate on the graphene sheet. I can't find a lot of information about evaporation of molecules using GROMACS. I would be really grateful If somebody can guide me, where to search or to get the below information: 1. how to put the graphene sheet inside the box if i only have its topology file .itp. 2. how to perform the evaporation process itself, knowing that I have the .pdb and the .itp file for the molecule that I want to evaporate. Thanks, Mohamed On Fri, Feb 7, 2020 at 1:23 AM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Hi, > What .itp file you have .. > > On Tue 4 Feb, 2020, 4:44 PM Mohamed Abdelaal, > wrote: > > > Hello everybody :) > > > > I want to know how to simulate a graphene sheet in GROMOS 54A7 and get > the > > .top file knowing that I have the .itp file. > > > > Thanks > > Mohamed > > -- > > 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.
[gmx-users] Graphene Sheet in GROMOS 54A7
Hello everybody :) I want to know how to simulate a graphene sheet in GROMOS 54A7 and get the .top file knowing that I have the .itp file. Thanks Mohamed -- 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.
