Re: [gmx-users] how to repeat simulation correctly?
On Thu, Nov 22, 2012 at 10:13 AM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... An MD simulation is normally deterministic, inasmuch as the inputs and algorithm determine the output, even if the model physics being simulated is not determinstic (e.g. stochastic elements to the integration). One needs to be clear about which aspect is of interest. The simulation is often not reproducible, either, because of run-time effects like dynamic load balancing or differences in hardware/compilers/libraries. And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Of course, sampling a coloured ball from a bag of balls, putting it back in without letting go, and taking it back out doesn't create a new sample from the bag. If all the balls were slowly changing colour and you were trying to sample the distribution of colours, then that in-and-out process might be a way to create a new sample, but it depends on the timescales involved... So yes, you could start from the same set of positions and velocities and rely on run-time irreproducibility to introduce differences, and chaos to amplify those over simulation time, in order to reach points from which you could make statistically independent simulations. Empirically, you'll need less simulation time to reach that point if you take active steps to make a significant difference, like changing the velocity of every atom. You need to re-equilibrate each time you perturb, but that's generally cheaper than the alternatives. Mark Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists --**- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se
Re: [gmx-users] how to repeat simulation correctly?
Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Not to forget about the additional stochastic term in the V-rescale thermostat, when it's used. Since the equations are evidently deterministic, is the chaotic nature of MD just a numerical effect? The practical point: if the velocities are reset upon a restart from an equilibrated frame in order to generate multiple, independent trajectories for statistical purposes, the equilibration will be probably lost and a new equilibration phase will be needed. Is this correct? Best, Felipe On 11/22/2012 11:12 AM, Erik Marklund wrote: It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
MD is chaotic regardless of how differences, however small, are created in the first place. This was just one example. Stochastic terms in e.g. the v-rescale thermostat will rely on the same sequence of random numbers in separate simulations if the random number generator is seeded in the same way. But sure, choosing different seeds would be one way of having diverging simulations. I think your point is correct in principle, e.g. when pressure is concerned. That equilibration time must however also be put in relation to how long it takes for two simulations to become uncorrelated. Best, Erik 22 nov 2012 kl. 11.30 skrev Felipe Pineda, PhD: Not to forget about the additional stochastic term in the V-rescale thermostat, when it's used. Since the equations are evidently deterministic, is the chaotic nature of MD just a numerical effect? The practical point: if the velocities are reset upon a restart from an equilibrated frame in order to generate multiple, independent trajectories for statistical purposes, the equilibration will be probably lost and a new equilibration phase will be needed. Is this correct? Best, Felipe On 11/22/2012 11:12 AM, Erik Marklund wrote: It will depend on the integration algorithms, parallelization, etc. The equations are deterministic, but numerical differences may arise e.g. from different ordering of floating point numbers being added together in different simulations. The chaotic nature of MD would then have the simulations diverge over time, but the question is how long it takes for such differences to really manifest. Best, Erik 22 nov 2012 kl. 10.13 skrev Felipe Pineda, PhD: Would non-deterministic be correct to characterize the nature of MD as well? There is also deterministic chaos ... And what about the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different, independent trajectories even if restarted from a previous, equilibrated frame even without resetting velocities, i.e., as a continuation run using the velocities recorded in the gro file of the selected snapshot? Felipe On 11/22/2012 12:55 AM, Mark Abraham wrote: Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688
Re: [gmx-users] how to repeat simulation correctly?
If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- +---+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Computational Chemistry and | | Biochemistry Laboratory | | School of Natural Sciences| | Linnaeus University | | SE-391 82 Kalmar | | Norrgård, room 311| | Sweden - Sverige | | Phone: ++46-480-44 6329 | | Mobile: ++46-76-8420572 | | E-Mail: luis.pinedadecas...@lnu.se| | Web:lnu.se| +---+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] how to repeat simulation correctly?
Generating velocities from a new random seed is normally regarded as good enough. By the time you equilibrate, the chaotic nature of MD starts to work for you. Mark On Nov 21, 2012 1:04 PM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: So how would you repeat the (let be it converged) simulation from different starting conditions in order to add that valuable statistics you mention? I think this was Albert's question Felipe On 11/21/2012 12:41 PM, Mark Abraham wrote: If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation). Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert mailmd2...@gmail.com wrote: hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Listshttp://www.gromacs.org/**Support/Mailing_Lists http://**www.gromacs.org/Support/**Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- +-**--+ | Luis Felipe Pineda De Castro, PhD | | Computational Chemist - Postdoc | | Computational Chemistry and | | Biochemistry Laboratory | | School of Natural Sciences| | Linnaeus University | | SE-391 82 Kalmar | | Norrgård, room 311| | Sweden - Sverige | | Phone: ++46-480-44 6329 | | Mobile: ++46-76-8420572 | | E-Mail: luis.pinedadecas...@lnu.se| | Web:lnu.se| +-**--+ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] how to repeat simulation correctly?
hello: I am quite confused on how to repeat our MD in Gromacs. If we started from the same equilibrated .gro file with gen_vel= no in md.mdp, we may get exactly the same results which cannot be treated as reasonable repeated running. However, if we use gen_vel=yes for each round of running, sometimes our simulation may not converged at our simulated time scale and we may get two results with large differences. So I am just wondering how to perform repeated MD in Gromacs in a correct way so that our results can be acceptably repeated? thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
