Re: [gmx-users] What is the "gen-vel" used for?
Yeping Sun, Quoting Justin's answer for a similar question I had on how to repeat a simulation say 10 times " To run 10 independent simulations, I would run minimization once and start from 10 new equilibration runs, each with a different set of initial velocities (change gen_seed or simply set to -1).That approach may not be as robust as starting from 10 different configurations, but the exact approach depends on the system in question". -- 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] What is the "gen-vel" used for?
On 1/2/20 10:07 PM, Sun Yeping wrote: I guess I understand what you mean, but could you clarify it further? I usually perform the simulations by the following process: (1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints; (3) NPT for 1 ns with heavy atom restrains; (4) production simulation without restraints. To prove repeatability, I think I need to set up several parallel simulations. Could I perform the NPT step for 3 different durations such as 1 ns, 2 ns, 5 ns to get three different velocities at the final frame of the three NPT simulations, and remove the restraints and continue the simulation from these velocities respectively? Thus I will get three production simulations start from different velocities. Or do I need to stop a so-called production simulations (without restraint) at different time points and get three configurations, and repeat the EM, NVT, NPT and production simulation steps for the three configurations respectively to get three independent trajectories? The conventional approach is to generate velocities at the beginning of what you have defined as step (2) above. Continuing NPT is basically just taking time points of the same run and continuing it. One could argue that those simulations will eventually diverge, but I don't think you can truly call them independent runs. They all started from the exact same input/state but were just allowed to run for different amounts of time. -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] What is the "gen-vel" used for?
I guess I understand what you mean, but could you clarify it further? I usually perform the simulations by the following process: (1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints; (3) NPT for 1 ns with heavy atom restrains; (4) production simulation without restraints. To prove repeatability, I think I need to set up several parallel simulations. Could I perform the NPT step for 3 different durations such as 1 ns, 2 ns, 5 ns to get three different velocities at the final frame of the three NPT simulations, and remove the restraints and continue the simulation from these velocities respectively? Thus I will get three production simulations start from different velocities. Or do I need to stop a so-called production simulations (without restraint) at different time points and get three configurations, and repeat the EM, NVT, NPT and production simulation steps for the three configurations respectively to get three independent trajectories? Best regards, Yeping On Fri, Jan 3, 2020 at 9:50 AM Justin Lemkul wrote: > > > On 1/2/20 8:25 PM, Sun Yeping wrote: > > Hello Justin, > > > > Your reply is very helpful. I can understand the first method for proving > > repeatablity: use a different initial configuration. But how to set the > > different initial velocities with the same initial configuration if not > > using the "gen-vel" option in the .mdp file for the production > simulations? > > Again, you don't generate velocities at the outset of a "production" > simulation. You're creating a randomized system that needs to be > re-equilibrated. Hence, velocities are only ever generated at the outset > of the first step of equilibration. Perhaps this is just a discrepancy > in terminology, but one cannot justifiably start a "production" > simulation (i.e. one in which data are collected) from a totally random > state that may not even be stable. > > -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] What is the "gen-vel" used for?
On 1/2/20 8:25 PM, Sun Yeping wrote: Hello Justin, Your reply is very helpful. I can understand the first method for proving repeatablity: use a different initial configuration. But how to set the different initial velocities with the same initial configuration if not using the "gen-vel" option in the .mdp file for the production simulations? Again, you don't generate velocities at the outset of a "production" simulation. You're creating a randomized system that needs to be re-equilibrated. Hence, velocities are only ever generated at the outset of the first step of equilibration. Perhaps this is just a discrepancy in terminology, but one cannot justifiably start a "production" simulation (i.e. one in which data are collected) from a totally random state that may not even be stable. -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] What is the "gen-vel" used for?
Hello Justin, Your reply is very helpful. I can understand the first method for proving repeatablity: use a different initial configuration. But how to set the different initial velocities with the same initial configuration if not using the "gen-vel" option in the .mdp file for the production simulations? Best regards, Yeping -- 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] What is the "gen-vel" used for?
On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul wrote: > > > On 12/30/19 11:11 PM, sunyeping wrote: > > Hello Justin, > > > > Thank you for your reply. > > > > If I need to prove the repeatability of a phenonmenon (such as the > > peptide folding pathway or a conformational transition) in > > simulations, is it reasonable to run the production MD several times > > and each time the simulation is continued for the same NPT > > equilibration? Do I need to introduce centain random factors (if not > > the velocity) in each production simulation? > > > > No, because those aren't independent observations. You're just running > the same .tpr file over and over again, which will diverge slightly for > numerical reasons but these are not true replicate simulations. If you > want to prove repeatability, you need to repeat exactly what you did in > the first case multiple times, with the only difference being either (1) > a different initial configuration or (2) the same configuration with > different initial velocities. The initial condition is what needs to > change, and then you need to equilibrate and perform the simulation the > same way to see if the same behavior arises. > > -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] What is the "gen-vel" used for?
On 12/30/19 11:11 PM, sunyeping wrote: Hello Justin, Thank you for your reply. If I need to prove the repeatability of a phenonmenon (such as the peptide folding pathway or a conformational transition) in simulations, is it reasonable to run the production MD several times and each time the simulation is continued for the same NPT equilibration? Do I need to introduce centain random factors (if not the velocity) in each production simulation? No, because those aren't independent observations. You're just running the same .tpr file over and over again, which will diverge slightly for numerical reasons but these are not true replicate simulations. If you want to prove repeatability, you need to repeat exactly what you did in the first case multiple times, with the only difference being either (1) a different initial configuration or (2) the same configuration with different initial velocities. The initial condition is what needs to change, and then you need to equilibrate and perform the simulation the same way to see if the same behavior arises. -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] What is the "gen-vel" used for?
Hello Justin, Thank you for your reply. If I need to prove the repeatability of a phenonmenon (such as the peptide folding pathway or a conformational transition) in simulations, is it reasonable to run the production MD several times and each time the simulation is continued for the same NPT equilibration? Do I need to introduce centain random factors (if not the velocity) in each production simulation? Best regards Yeping -- From:Justin Lemkul Sent At:2019 Dec. 31 (Tue.) 11:53 To:gromacs ; 孙业平 Subject:Re: [gmx-users] What is the "gen-vel" used for? On 12/30/19 10:14 PM, sunyeping wrote: > Dear all, > > In the molecular dynamics parameters (.mdp option) section of the Gromacs > user guide > (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), > there is an introduction of the "gen-vel" option. According to the > introduction, if set to "yes", it will generate velocities in gmx grompp > according to a Maxwell distribution at temperature gen-temp, with random seed > gen-seed. > > However I don't understand why we should need the velocities. Is it used to > generate different trajectories when running similations with the same system > because in each run the "gen-vol" can give a different random velocity? But > will the trajectories exactly the same if we set the "gen-vel" option to > "no" ? I think that the production MD with a system should be repeated for > several times in order to get convincing results, then should I set the > "gen-vol" option to "yes" or "no" for these repeative MD? gen-vel is only ever used at the outset of equilibration, when there are no other velocities. All you have are coordinates, but to start the simulation, you need velocities. At all other stages of the simulation protocol, gen-vel should be set to "no," otherwise you're just breaking the simulation by introducing a discontinuity. > I try to set the "gen-vel" option to "yes", but when running the grommp to > generate the tpr file like: > gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o > md.tpr > > I get the following warning and fatal error caused by the warning: > WARNING 1 [file md.mdp]: >You are generating velocities so I am assuming you are equilibrating a >system. You are using Parrinello-Rahman pressure coupling, but this can >be unstable for equilibration. If your system crashes, try equilibrating >first with Berendsen pressure coupling. If you are not equilibrating the >system, you can probably ignore this warning. > > Fatal error: > Too many warnings (1). > If you are sure all warnings are harmless, use the -maxwarn option. > > Does it mean that "gen-vel" is usually used for equilibrating but no for > production simulation? If I am running a production simulation, should I use > the -maxwarn option to ignore the warning? Never use -maxwarn. Seriously. It's probably bad that this option even exists. Think about it - you already have velocities in the checkpoint file. Why would you generate new velocities? -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] What is the "gen-vel" used for?
On 12/30/19 10:14 PM, sunyeping wrote: Dear all, In the molecular dynamics parameters (.mdp option) section of the Gromacs user guide (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), there is an introduction of the "gen-vel" option. According to the introduction, if set to "yes", it will generate velocities in gmx grompp according to a Maxwell distribution at temperature gen-temp, with random seed gen-seed. However I don't understand why we should need the velocities. Is it used to generate different trajectories when running similations with the same system because in each run the "gen-vol" can give a different random velocity? But will the trajectories exactly the same if we set the "gen-vel" option to "no" ? I think that the production MD with a system should be repeated for several times in order to get convincing results, then should I set the "gen-vol" option to "yes" or "no" for these repeative MD? gen-vel is only ever used at the outset of equilibration, when there are no other velocities. All you have are coordinates, but to start the simulation, you need velocities. At all other stages of the simulation protocol, gen-vel should be set to "no," otherwise you're just breaking the simulation by introducing a discontinuity. I try to set the "gen-vel" option to "yes", but when running the grommp to generate the tpr file like: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr I get the following warning and fatal error caused by the warning: WARNING 1 [file md.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. Does it mean that "gen-vel" is usually used for equilibrating but no for production simulation? If I am running a production simulation, should I use the -maxwarn option to ignore the warning? Never use -maxwarn. Seriously. It's probably bad that this option even exists. Think about it - you already have velocities in the checkpoint file. Why would you generate new velocities? -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.
[gmx-users] What is the "gen-vel" used for?
Dear all, In the molecular dynamics parameters (.mdp option) section of the Gromacs user guide (http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html), there is an introduction of the "gen-vel" option. According to the introduction, if set to "yes", it will generate velocities in gmx grompp according to a Maxwell distribution at temperature gen-temp, with random seed gen-seed. However I don't understand why we should need the velocities. Is it used to generate different trajectories when running similations with the same system because in each run the "gen-vol" can give a different random velocity? But will the trajectories exactly the same if we set the "gen-vel" option to "no" ? I think that the production MD with a system should be repeated for several times in order to get convincing results, then should I set the "gen-vol" option to "yes" or "no" for these repeative MD? I try to set the "gen-vel" option to "yes", but when running the grommp to generate the tpr file like: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md.tpr I get the following warning and fatal error caused by the warning: WARNING 1 [file md.mdp]: You are generating velocities so I am assuming you are equilibrating a system. You are using Parrinello-Rahman pressure coupling, but this can be unstable for equilibration. If your system crashes, try equilibrating first with Berendsen pressure coupling. If you are not equilibrating the system, you can probably ignore this warning. Fatal error: Too many warnings (1). If you are sure all warnings are harmless, use the -maxwarn option. Does it mean that "gen-vel" is usually used for equilibrating but no for production simulation? If I am running a production simulation, should I use the -maxwarn option to ignore the warning? Thank you in advance. Best regards. Yeping Sun -- 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.
