Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi all, One of the conceptual difference between Berendsen and Nose-Hoover (NH), is the following. NH is basically a second order relaxation to the target temperature, which implies an oscillatory behavior. Berendsen is a first order relaxation (exponential type of behavior). This is preferable when the initial temperature is far from the target temperature, in which case NH is likely to produce large oscillations and, in general, take longer to equilibrate. Hence the practice to use Berendsen for the first part of the equilibration, and NH for production. There are still papers published on the subject in the "alive" literature. For example there is an analysis of the Berendsen dynamics in Morishita, JCP 113 (8) : 2976 (2000) In short, he finds approximate expressions for the configurational part of the state distribution function. It essentially varies between canonical for exceedingly small time constants (of the order of the timestep) to microcanonical for very large time constants. The distribution of momenta remains unknown. In addition to the average temperature, the temperature fluctuations expected for the NVT ensemble must be reproduced in the simulation. Nose-Hoover was shown to do this correctly. This could be important when studying the stability of a conformation for example. Now concerning Chris' question: [EMAIL PROTECTED] wrote: Have you seen any information to suggest that this is actually a non-trivial conce"rn? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? There are two aspects here: (a) point charges and LJ force, which constitute the physical model, and (b) the cutoffs and such, which are simulation artefacts and disrupt the physics of the model (by allowing creation of energy, etc...). My opinion is that, given a physical model (even approximate), one should simulate the dynamics as accurately as possible, in order to produce the thermodynamical ensemble corresponding to the underlying physical model. Before plugging in the thermostat, one should check that the simulation conserves energy "not too bad"(using PME or switch functions, etc...). Now if there is still an energy drift, the thermostat will absorb the excess energy, and the system will end up in a non-equilibrium steady state, with a heat well (cutoffs, etc) and a heat sink (thermostat). The good side is that the NH thermostat was shown (by Hoover himself) to produce a stationary canonical distribution even in a non-equilibrium case. Sorry for the long email :) Michel -- == Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland http://ludwig-sun1.unil.ch/~mcuendet == ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
David Osguthorpe wrote: On Tue, Jul 22, 2008 at 11:16:21PM -0400, [EMAIL PROTECTED] wrote: Thanks David for sharing your knowledge, especially the note that for further information one can refer to the literature that was written around the time that these thermostats were released. I have a question though: I was just trying to correct the impression from the posts that the issue with Berendsen is some urban legend - it is not and there is extensive literature on it - even if its not googleable by the way it is also true that if you use a thermostat or barostat then although long time averages are equivalent to averages in the NVT or NPT ensemble strictly the dynamics is no longer valid as a Newtonian trajectory so you should not derive dynamic properties >from such trajectories. Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? I think the response by Michael says it as well as I could - this was a point made by some of these papers - so just because the averages are valid does not mean the dynamics is valid - you are right in that it may not be something that has an observable effect with current simulations but it is some form of artifact that may bias the simulations consistently whereas eg. with force fields you can have lots of cancellation of errors Cancellation of errors is not an excuse for poor force fields. In addition, built-in cut-offs for some force fields also give systematic bias, but this is beside the point. Although it is indeed well-known that Berendsen thermostat (and Barostat!) create significant artifacts, these are not as bad as they used to be, in particular due to the use of PME. Temperature coupling hardly does anything at all when using PME, which you can verify by plotting the temperature scaling factor as a function of time. So we are all waiting for a healthy volunteer to implement the latest and greatest algorithms in the latest and greatest gromacs development code. Cheers, -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
On Tue, Jul 22, 2008 at 11:16:21PM -0400, [EMAIL PROTECTED] wrote: > Thanks David for sharing your knowledge, especially the note that for > further information one can refer to the literature that was written > around the time that these thermostats were released. I have a > question though: I was just trying to correct the impression from the posts that the issue with Berendsen is some urban legend - it is not and there is extensive literature on it - even if its not googleable > > >by the way it is also true that if you use a thermostat or barostat > >then although long time averages are equivalent to averages in the > >NVT or NPT ensemble strictly the dynamics is no longer valid as > >a Newtonian trajectory so you should not derive dynamic properties > >from such trajectories. > > Have you seen any information to suggest that this is actually a > non-trivial concern? That is, given static point charges, an empirical > LJ force, short cutoffs, etc., do you believe that the application of > nose-hoover, berendsen, or even the arbitrary velocity rescaling > significantly degrades the quality of the obtained dynamics? > I think the response by Michael says it as well as I could - this was a point made by some of these papers - so just because the averages are valid does not mean the dynamics is valid - you are right in that it may not be something that has an observable effect with current simulations but it is some form of artifact that may bias the simulations consistently whereas eg. with force fields you can have lots of cancellation of errors David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Thanks David for sharing your knowledge, especially the note that for further information one can refer to the literature that was written around the time that these thermostats were released. I have a question though: by the way it is also true that if you use a thermostat or barostat then although long time averages are equivalent to averages in the NVT or NPT ensemble strictly the dynamics is no longer valid as a Newtonian trajectory so you should not derive dynamic properties from such trajectories. Have you seen any information to suggest that this is actually a non-trivial concern? That is, given static point charges, an empirical LJ force, short cutoffs, etc., do you believe that the application of nose-hoover, berendsen, or even the arbitrary velocity rescaling significantly degrades the quality of the obtained dynamics? Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
On Mon, Jul 21, 2008 at 11:46:00PM -0400, Justin A. Lemkul wrote: > > I too rely heavily on the Berendsen methods for T- and P-coupling, and have > always found them satisfactory. I have not seen much beyond the casual > references to the fact that N-H T-coupling and Parrinello-Rahman P-coupling > are superior in terms of membrane simulations. I have tried both, and have > found both setups to be equally reasonable in their results. It seems, > overall, that Nose-Hoover schemes are often applied using NAMD and CHARMM > software. I don't know if this choice is motivated by the software, or the > force fields used. > > There are a few casual references to Berendsen being less than optimal in > the literature and in archived presentation materials (which I can probably > unearth if I can recall my Googling :). > In an attempt to correct some mis-information that seems to exist here. The question is whether you want to do science or to play. There are extensive references from the 80s as to why the Berendsen thermostat is invalid (unfortunately probably in the "lost" literature ie. that literature only available in paper form in those weird institutions called libraries) Hoover and others e.g. Andersen (J.Chem.Phys. 72, 2384, 1980) developed thermostats and barostats that they mathematically proved lead to NVT or NPT averages over long timescales (i.e. not by running simulations) no such proof exists for the Berendsen thermostat - nor even which ensemble long time averages belong to - it is a simple extension of the early arbitrary velocity scaling that was used in dynamics programs - hence it is scientifically strictly "invalid" and lead to the "less than optimal" references. - this is probably why CHARMM and NAMD use Nose-Hoover - it certainly has nothing to do with force fields You should also try and get a copy of the book Computer Simulation of Liquids by Allen and Tildesley 1987 on page 232 it discusses the difference between the Berendsen and Hoover thermostats - essentially in the Berendsen thermostat the velocity scale factor directly depends on the current temperature difference whereas for the Hoover its the rate of change with time (ie. time derivative) of the velocity scale factor that depends on the current temperature difference by the way it is also true that if you use a thermostat or barostat then although long time averages are equivalent to averages in the NVT or NPT ensemble strictly the dynamics is no longer valid as a Newtonian trajectory so you should not derive dynamic properties from such trajectories. This is from actually reading a lot of this literature at the time when the first comments were made about the Berendsen thermostat. David ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Chris, I too rely heavily on the Berendsen methods for T- and P-coupling, and have always found them satisfactory. I have not seen much beyond the casual references to the fact that N-H T-coupling and Parrinello-Rahman P-coupling are superior in terms of membrane simulations. I have tried both, and have found both setups to be equally reasonable in their results. It seems, overall, that Nose-Hoover schemes are often applied using NAMD and CHARMM software. I don't know if this choice is motivated by the software, or the force fields used. There are a few casual references to Berendsen being less than optimal in the literature and in archived presentation materials (which I can probably unearth if I can recall my Googling :). Based on experience, I too would agree that Berendsen suffices, and only made mention of the N-H argument as a talking point, something that others have argued. If I come across any of these references again, I will be sure to post them to the list to continue the discussion. -Justin [EMAIL PROTECTED] wrote: Hi Justin, I wonder if you could expand upon the following statement, or perhaps offer some links or references. "Some argument can be made that N-H is more applicable to membrane simulations." I am interested because I use a Berendsen thermostat for membrane simulations. To be entirely honest, I have no particular understanding of the consequence of this choice beyond the oft-heard statement that Berendsen T-coupling doesn't yield the correct ensemble. But it is very intuitive and, as you say, it's usage is quite common and I have thus far relied on these points to guide my choice of temperature-coupling algorithm. Therefore I am hoping to take advantage of this opportunity to learn a bit more about temperature coupling as you seem to understand it quite well. I am hoping that you can outline the logic underlying the 'correct ensemble' statement and indicate how this is especially applicable to membrane simulations. I do realize that this is a large request on this type of mailing list. Please feel free to decline. Much obliged, Chris. -- original message -- I have used the Berendsen method almost exclusively in my simulations, and it is widely used in most of the literature I read. While the argument can be made that Nose-Hoover gives a result closer to the true ensemble than Berendsen, I think both are sufficient for simple protein in water simulations. Some argument can be made that N-H is more applicable to membrane simulations. As for whether or not you need to slowly increase the temperature, it is really up to you. Usually such rigor is not necessary, as often position restraints are applied to the protein during initial equilibration. I have never experienced any adverse effects of simply setting the initial temperature, although that's not to say it's not possible :) Just my $0.02. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi Justin, I wonder if you could expand upon the following statement, or perhaps offer some links or references. "Some argument can be made that N-H is more applicable to membrane simulations." I am interested because I use a Berendsen thermostat for membrane simulations. To be entirely honest, I have no particular understanding of the consequence of this choice beyond the oft-heard statement that Berendsen T-coupling doesn't yield the correct ensemble. But it is very intuitive and, as you say, it's usage is quite common and I have thus far relied on these points to guide my choice of temperature-coupling algorithm. Therefore I am hoping to take advantage of this opportunity to learn a bit more about temperature coupling as you seem to understand it quite well. I am hoping that you can outline the logic underlying the 'correct ensemble' statement and indicate how this is especially applicable to membrane simulations. I do realize that this is a large request on this type of mailing list. Please feel free to decline. Much obliged, Chris. -- original message -- I have used the Berendsen method almost exclusively in my simulations, and it is widely used in most of the literature I read. While the argument can be made that Nose-Hoover gives a result closer to the true ensemble than Berendsen, I think both are sufficient for simple protein in water simulations. Some argument can be made that N-H is more applicable to membrane simulations. As for whether or not you need to slowly increase the temperature, it is really up to you. Usually such rigor is not necessary, as often position restraints are applied to the protein during initial equilibration. I have never experienced any adverse effects of simply setting the initial temperature, although that's not to say it's not possible :) Just my $0.02. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
I have used the Berendsen method almost exclusively in my simulations, and it is widely used in most of the literature I read. While the argument can be made that Nose-Hoover gives a result closer to the true ensemble than Berendsen, I think both are sufficient for simple protein in water simulations. Some argument can be made that N-H is more applicable to membrane simulations. As for whether or not you need to slowly increase the temperature, it is really up to you. Usually such rigor is not necessary, as often position restraints are applied to the protein during initial equilibration. I have never experienced any adverse effects of simply setting the initial temperature, although that's not to say it's not possible :) Just my $0.02. -Justin [EMAIL PROTECTED] wrote: Hi Lin! I personally feel increasing the temperature in increments better than giving sudden temperature jump to protein. Regarding temp coupling, both have their limitations. Berendsen is a weak coupling, so can be used for initial runs. Later you can use Nose-Hoover after the proper equilibration is done. However, in case of Nose-Hoover, you might have to select the tau_t carefully, or you will get very large oscillations. PS: Others please do correct me, if I will be thinking a bit wrong somewhere. Cheers! Monika On Mon, 21 Jul 2008, Chih-Ying Lin wrote: Hi My system has been dealt with minimisation and the system was kept constant at 0 K. Then, I want to increate the temperature to 300 K using the Berendsen thermostat. Should I increase the temperature of the system step by step... ? increase temp from 0 K to 50 K 51 K - 100 K 101 K - 150 K 151 K - 200 K 201 K - 250 K 251 K - 300 K seperately? or increase temp from 0 K to 300 K at one time? After the temperature of the system reaches 300 K, should I use Nose-Hoover temperature coupling to keep the system at the equliibration on 300 K? I have read manual though. Thanks a lot Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi Lin! I personally feel increasing the temperature in increments better than giving sudden temperature jump to protein. Regarding temp coupling, both have their limitations. Berendsen is a weak coupling, so can be used for initial runs. Later you can use Nose-Hoover after the proper equilibration is done. However, in case of Nose-Hoover, you might have to select the tau_t carefully, or you will get very large oscillations. PS: Others please do correct me, if I will be thinking a bit wrong somewhere. Cheers! Monika On Mon, 21 Jul 2008, Chih-Ying Lin wrote: Hi My system has been dealt with minimisation and the system was kept constant at 0 K. Then, I want to increate the temperature to 300 K using the Berendsen thermostat. Should I increase the temperature of the system step by step... ? increase temp from 0 K to 50 K 51 K - 100 K 101 K - 150 K 151 K - 200 K 201 K - 250 K 251 K - 300 K seperately? or increase temp from 0 K to 300 K at one time? After the temperature of the system reaches 300 K, should I use Nose-Hoover temperature coupling to keep the system at the equliibration on 300 K? I have read manual though. Thanks a lot Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Question about Berendsen thermostat and Nose-Hoover temp coupling
Hi My system has been dealt with minimisation and the system was kept constant at 0 K. Then, I want to increate the temperature to 300 K using the Berendsen thermostat. Should I increase the temperature of the system step by step... ? increase temp from 0 K to 50 K 51 K - 100 K 101 K - 150 K 151 K - 200 K 201 K - 250 K 251 K - 300 K seperately? or increase temp from 0 K to 300 K at one time? After the temperature of the system reaches 300 K, should I use Nose-Hoover temperature coupling to keep the system at the equliibration on 300 K? I have read manual though. Thanks a lot Lin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
