Re: [gmx-users] convergence of PMF
Hi, Thank you for the comments. That was really helpful. On Fri, Nov 17, 2017 at 7:22 PM, Peter Kroon <p.c.kr...@rug.nl> wrote: > > > On 17-11-17 14:48, Justin Lemkul wrote: > > > > > > On 11/17/17 8:47 AM, Peter Kroon wrote: > >> > >> On 17-11-17 14:38, Justin Lemkul wrote: > >>> > >>> On 11/17/17 6:28 AM, abhisek Mondal wrote: > >>>> Hello, > >>>> > >>>> I understand the invariant trend is the key feature to look out for > >>>> in this > >>>> case. > >>>> > >>>> But, is it possible to comment on the convergence from Force-vs-Time > >>>> plot ? > >>>> I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of > >>>> pulling the force became zero and thus the biasing potential goes > >>>> also to > >>>> zero. Hence, after 5 nm of dissociation the PMF should attain > >>>> convergence > >>>> if also invariant trend-line is found near that point. > >>>> > >>>> Does this explanation make any sense from convergence of PMF's > >>>> perspective ? > >>> No, because you're conducting a non-equilibrium process, which is not > >>> going to give you a PMF. > >>> > >>> Your system is changing over time due to the application of a biasing > >>> potential. It does not make sense to say that anything there converged > >>> based on any time-dependent quantity. > >> But shouldn't you be able to look at the force-vs-time profiles of your > >> windows? So that you can at least say that the force per window is > >> equilibrated? > > > > The OP mentioned a PMF, which is equilibrium sampling and indeed you > > *could* look at those forces, but then in this post it is mentioned > > that it's a non-equilibrium SMD simulation (non-zero pull rate), so > > no, there's nothing useful to look at here. > > > > I would also just bypass the forces anyway, since they are extremely > > noisy, and compute the PMF over different windows of time. That's the > > most straightforward way to look at convergence (and what reviewers > > *always* ask to see in papers). > Cheers, thanks for your insight. > > Peter > > > > -Justin > > > >> Peter > >> > >>> -Justin > >>> > >>>> > >>>> On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov > > > >>>> wrote: > >>>> > >>>>> One way to get some degree of confidence is to use the > >>>>> bootstrapping/error > >>>>> analysis options provided in gmx wham. But Justin is right you are > >>>>> looking > >>>>> for time invariance. So: use the first portion of your trajectory > >>>>> (say > >>>>> first 60%) and compute the PMF, then use the first 65% of your > >>>>> trajectory > >>>>> and see if it has changed (and by how much), then 70%, and 80% and > >>>>> so on. > >>>>> If you have converged (within reason), you should see that at some > >>>>> point, > >>>>> as you add more time to the analysis the PMF doesn't change (in any > >>>>> statistically significant way), when that occurs you have > >>>>> "converged". > >>>>> > >>>>> > >>>>> === > >>>>> Micholas Dean Smith, PhD. > >>>>> Post-doctoral Research Associate > >>>>> University of Tennessee/Oak Ridge National Laboratory > >>>>> Center for Molecular Biophysics > >>>>> > >>>>> > >>>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > >>>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of > >>>>> Justin > >>>>> Lemkul <jalem...@vt.edu> > >>>>> Sent: Thursday, November 16, 2017 8:04 AM > >>>>> To: gmx-us...@gromacs.org > >>>>> Subject: Re: [gmx-users] convergence of PMF > >>>>> > >>>>> On 11/16/17 3:34 AM, abhisek Mondal wrote: > >>>>>> Hi, > >>>>>> > >>>>>>I have derived a PMF (protein-ligand) using umbrella sampling > >>>>> method. &
Re: [gmx-users] convergence of PMF
On 17-11-17 14:48, Justin Lemkul wrote: > > > On 11/17/17 8:47 AM, Peter Kroon wrote: >> >> On 17-11-17 14:38, Justin Lemkul wrote: >>> >>> On 11/17/17 6:28 AM, abhisek Mondal wrote: >>>> Hello, >>>> >>>> I understand the invariant trend is the key feature to look out for >>>> in this >>>> case. >>>> >>>> But, is it possible to comment on the convergence from Force-vs-Time >>>> plot ? >>>> I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of >>>> pulling the force became zero and thus the biasing potential goes >>>> also to >>>> zero. Hence, after 5 nm of dissociation the PMF should attain >>>> convergence >>>> if also invariant trend-line is found near that point. >>>> >>>> Does this explanation make any sense from convergence of PMF's >>>> perspective ? >>> No, because you're conducting a non-equilibrium process, which is not >>> going to give you a PMF. >>> >>> Your system is changing over time due to the application of a biasing >>> potential. It does not make sense to say that anything there converged >>> based on any time-dependent quantity. >> But shouldn't you be able to look at the force-vs-time profiles of your >> windows? So that you can at least say that the force per window is >> equilibrated? > > The OP mentioned a PMF, which is equilibrium sampling and indeed you > *could* look at those forces, but then in this post it is mentioned > that it's a non-equilibrium SMD simulation (non-zero pull rate), so > no, there's nothing useful to look at here. > > I would also just bypass the forces anyway, since they are extremely > noisy, and compute the PMF over different windows of time. That's the > most straightforward way to look at convergence (and what reviewers > *always* ask to see in papers). Cheers, thanks for your insight. Peter > > -Justin > >> Peter >> >>> -Justin >>> >>>> >>>> On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov> >>>> wrote: >>>> >>>>> One way to get some degree of confidence is to use the >>>>> bootstrapping/error >>>>> analysis options provided in gmx wham. But Justin is right you are >>>>> looking >>>>> for time invariance. So: use the first portion of your trajectory >>>>> (say >>>>> first 60%) and compute the PMF, then use the first 65% of your >>>>> trajectory >>>>> and see if it has changed (and by how much), then 70%, and 80% and >>>>> so on. >>>>> If you have converged (within reason), you should see that at some >>>>> point, >>>>> as you add more time to the analysis the PMF doesn't change (in any >>>>> statistically significant way), when that occurs you have >>>>> "converged". >>>>> >>>>> >>>>> === >>>>> Micholas Dean Smith, PhD. >>>>> Post-doctoral Research Associate >>>>> University of Tennessee/Oak Ridge National Laboratory >>>>> Center for Molecular Biophysics >>>>> >>>>> >>>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of >>>>> Justin >>>>> Lemkul <jalem...@vt.edu> >>>>> Sent: Thursday, November 16, 2017 8:04 AM >>>>> To: gmx-us...@gromacs.org >>>>> Subject: Re: [gmx-users] convergence of PMF >>>>> >>>>> On 11/16/17 3:34 AM, abhisek Mondal wrote: >>>>>> Hi, >>>>>> >>>>>> I have derived a PMF (protein-ligand) using umbrella sampling >>>>> method. >>>>>> But how can I comment if the obtained PMF has converged well ? What >>>>>> are >>>>> the >>>>>> ways to check the convergence of a PMF ? >>>>> How would you check convergence of any quantity? You have to >>>>> determine >>>>> if the result is changing over time, and if it is invariant >>>>> (within the >>>>> context of available statistics), then the quantity is converged. >>>>> >>>>> -Justin >>>>> >>>>> -- >>
Re: [gmx-users] convergence of PMF
On 11/17/17 8:47 AM, Peter Kroon wrote: On 17-11-17 14:38, Justin Lemkul wrote: On 11/17/17 6:28 AM, abhisek Mondal wrote: Hello, I understand the invariant trend is the key feature to look out for in this case. But, is it possible to comment on the convergence from Force-vs-Time plot ? I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of pulling the force became zero and thus the biasing potential goes also to zero. Hence, after 5 nm of dissociation the PMF should attain convergence if also invariant trend-line is found near that point. Does this explanation make any sense from convergence of PMF's perspective ? No, because you're conducting a non-equilibrium process, which is not going to give you a PMF. Your system is changing over time due to the application of a biasing potential. It does not make sense to say that anything there converged based on any time-dependent quantity. But shouldn't you be able to look at the force-vs-time profiles of your windows? So that you can at least say that the force per window is equilibrated? The OP mentioned a PMF, which is equilibrium sampling and indeed you *could* look at those forces, but then in this post it is mentioned that it's a non-equilibrium SMD simulation (non-zero pull rate), so no, there's nothing useful to look at here. I would also just bypass the forces anyway, since they are extremely noisy, and compute the PMF over different windows of time. That's the most straightforward way to look at convergence (and what reviewers *always* ask to see in papers). -Justin Peter -Justin On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov> wrote: One way to get some degree of confidence is to use the bootstrapping/error analysis options provided in gmx wham. But Justin is right you are looking for time invariance. So: use the first portion of your trajectory (say first 60%) and compute the PMF, then use the first 65% of your trajectory and see if it has changed (and by how much), then 70%, and 80% and so on. If you have converged (within reason), you should see that at some point, as you add more time to the analysis the PMF doesn't change (in any statistically significant way), when that occurs you have "converged". === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, November 16, 2017 8:04 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] convergence of PMF On 11/16/17 3:34 AM, abhisek Mondal wrote: Hi, I have derived a PMF (protein-ligand) using umbrella sampling method. But how can I comment if the obtained PMF has converged well ? What are the ways to check the convergence of a PMF ? How would you check convergence of any quantity? You have to determine if the result is changing over time, and if it is invariant (within the context of available statistics), then the quantity is converged. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] convergence of PMF
On 17-11-17 14:38, Justin Lemkul wrote: > > > On 11/17/17 6:28 AM, abhisek Mondal wrote: >> Hello, >> >> I understand the invariant trend is the key feature to look out for >> in this >> case. >> >> But, is it possible to comment on the convergence from Force-vs-Time >> plot ? >> I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of >> pulling the force became zero and thus the biasing potential goes >> also to >> zero. Hence, after 5 nm of dissociation the PMF should attain >> convergence >> if also invariant trend-line is found near that point. >> >> Does this explanation make any sense from convergence of PMF's >> perspective ? > > No, because you're conducting a non-equilibrium process, which is not > going to give you a PMF. > > Your system is changing over time due to the application of a biasing > potential. It does not make sense to say that anything there converged > based on any time-dependent quantity. But shouldn't you be able to look at the force-vs-time profiles of your windows? So that you can at least say that the force per window is equilibrated? Peter > > -Justin > >> >> >> On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov> >> wrote: >> >>> One way to get some degree of confidence is to use the >>> bootstrapping/error >>> analysis options provided in gmx wham. But Justin is right you are >>> looking >>> for time invariance. So: use the first portion of your trajectory (say >>> first 60%) and compute the PMF, then use the first 65% of your >>> trajectory >>> and see if it has changed (and by how much), then 70%, and 80% and >>> so on. >>> If you have converged (within reason), you should see that at some >>> point, >>> as you add more time to the analysis the PMF doesn't change (in any >>> statistically significant way), when that occurs you have "converged". >>> >>> >>> === >>> Micholas Dean Smith, PhD. >>> Post-doctoral Research Associate >>> University of Tennessee/Oak Ridge National Laboratory >>> Center for Molecular Biophysics >>> >>> >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin >>> Lemkul <jalem...@vt.edu> >>> Sent: Thursday, November 16, 2017 8:04 AM >>> To: gmx-us...@gromacs.org >>> Subject: Re: [gmx-users] convergence of PMF >>> >>> On 11/16/17 3:34 AM, abhisek Mondal wrote: >>>> Hi, >>>> >>>> I have derived a PMF (protein-ligand) using umbrella sampling >>> method. >>>> But how can I comment if the obtained PMF has converged well ? What >>>> are >>> the >>>> ways to check the convergence of a PMF ? >>> How would you check convergence of any quantity? You have to determine >>> if the result is changing over time, and if it is invariant (within the >>> context of available statistics), then the quantity is converged. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> == >>> >>> -- >>> 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] convergence of PMF
On 11/17/17 6:28 AM, abhisek Mondal wrote: Hello, I understand the invariant trend is the key feature to look out for in this case. But, is it possible to comment on the convergence from Force-vs-Time plot ? I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of pulling the force became zero and thus the biasing potential goes also to zero. Hence, after 5 nm of dissociation the PMF should attain convergence if also invariant trend-line is found near that point. Does this explanation make any sense from convergence of PMF's perspective ? No, because you're conducting a non-equilibrium process, which is not going to give you a PMF. Your system is changing over time due to the application of a biasing potential. It does not make sense to say that anything there converged based on any time-dependent quantity. -Justin On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov> wrote: One way to get some degree of confidence is to use the bootstrapping/error analysis options provided in gmx wham. But Justin is right you are looking for time invariance. So: use the first portion of your trajectory (say first 60%) and compute the PMF, then use the first 65% of your trajectory and see if it has changed (and by how much), then 70%, and 80% and so on. If you have converged (within reason), you should see that at some point, as you add more time to the analysis the PMF doesn't change (in any statistically significant way), when that occurs you have "converged". === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, November 16, 2017 8:04 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] convergence of PMF On 11/16/17 3:34 AM, abhisek Mondal wrote: Hi, I have derived a PMF (protein-ligand) using umbrella sampling method. But how can I comment if the obtained PMF has converged well ? What are the ways to check the convergence of a PMF ? How would you check convergence of any quantity? You have to determine if the result is changing over time, and if it is invariant (within the context of available statistics), then the quantity is converged. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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 Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] convergence of PMF
Hello, I understand the invariant trend is the key feature to look out for in this case. But, is it possible to comment on the convergence from Force-vs-Time plot ? I mean, if I comment that using 0.01 nm ps-1 pull rate after 500 ps of pulling the force became zero and thus the biasing potential goes also to zero. Hence, after 5 nm of dissociation the PMF should attain convergence if also invariant trend-line is found near that point. Does this explanation make any sense from convergence of PMF's perspective ? On Thu, Nov 16, 2017 at 1:15 PM, Smith, Micholas D. <smit...@ornl.gov> wrote: > One way to get some degree of confidence is to use the bootstrapping/error > analysis options provided in gmx wham. But Justin is right you are looking > for time invariance. So: use the first portion of your trajectory (say > first 60%) and compute the PMF, then use the first 65% of your trajectory > and see if it has changed (and by how much), then 70%, and 80% and so on. > If you have converged (within reason), you should see that at some point, > as you add more time to the analysis the PMF doesn't change (in any > statistically significant way), when that occurs you have "converged". > > > === > Micholas Dean Smith, PhD. > Post-doctoral Research Associate > University of Tennessee/Oak Ridge National Laboratory > Center for Molecular Biophysics > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin > Lemkul <jalem...@vt.edu> > Sent: Thursday, November 16, 2017 8:04 AM > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] convergence of PMF > > On 11/16/17 3:34 AM, abhisek Mondal wrote: > > Hi, > > > > I have derived a PMF (protein-ligand) using umbrella sampling > method. > > But how can I comment if the obtained PMF has converged well ? What are > the > > ways to check the convergence of a PMF ? > > How would you check convergence of any quantity? You have to determine > if the result is changing over time, and if it is invariant (within the > context of available statistics), then the quantity is converged. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. > -- Abhisek Mondal *Senior Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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] convergence of PMF
One way to get some degree of confidence is to use the bootstrapping/error analysis options provided in gmx wham. But Justin is right you are looking for time invariance. So: use the first portion of your trajectory (say first 60%) and compute the PMF, then use the first 65% of your trajectory and see if it has changed (and by how much), then 70%, and 80% and so on. If you have converged (within reason), you should see that at some point, as you add more time to the analysis the PMF doesn't change (in any statistically significant way), when that occurs you have "converged". === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, November 16, 2017 8:04 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] convergence of PMF On 11/16/17 3:34 AM, abhisek Mondal wrote: > Hi, > > I have derived a PMF (protein-ligand) using umbrella sampling method. > But how can I comment if the obtained PMF has converged well ? What are the > ways to check the convergence of a PMF ? How would you check convergence of any quantity? You have to determine if the result is changing over time, and if it is invariant (within the context of available statistics), then the quantity is converged. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] convergence of PMF
On 11/16/17 3:34 AM, abhisek Mondal wrote: Hi, I have derived a PMF (protein-ligand) using umbrella sampling method. But how can I comment if the obtained PMF has converged well ? What are the ways to check the convergence of a PMF ? How would you check convergence of any quantity? You have to determine if the result is changing over time, and if it is invariant (within the context of available statistics), then the quantity is converged. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] convergence of PMF
Hi, you can check whether the forces of the windows (pullf.xvg files) have converged. Peter On 16-11-17 09:34, abhisek Mondal wrote: > Hi, > > I have derived a PMF (protein-ligand) using umbrella sampling method. > But how can I comment if the obtained PMF has converged well ? What are the > ways to check the convergence of a PMF ? > > Please help me out here. > > Thank you. > > -- 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.
