Re: [gmx-users] Re: Cross-correlation maps
Hey, In addition to Newton's cradle, there's also Columbus' egg. To make it stand, you smash it slightly, pressing one end. If you do PCA on that, you'll find a collective motion involving both the smashed end as well as the opposite, unscathed end. That accounts for the greater part of the global, end-to-end collective motions you see when you analyze the backbone. You don't have that when looking at the more subtle side chain motions. Cheers, Tsjerk On Tue, Aug 28, 2012 at 8:34 AM, Mark Abraham wrote: > On 28/08/2012 4:09 PM, James Starlight wrote: >> >> Mark, >> >> Thanks for explanation! >> >> >> 2012/8/27, Mark Abraham : >> >>> Did you construct a correlation matrix from side chain atoms? >> >> Yes, and there is some degree of correlation between adjacent side >> chains but lack of any cooperativety between distant side-chains. In >> comparison in that protein there were alot of cooperativity in motion >> of the distinct backbones. > > > Then that might be the conclusion, but that's your judgement to make from > the full context. It's hardly likely that there'd be magical "action at a > distance," but motion along the lines of Newton's cradle could have been > detected and would be fascinating to see in a protein (e.g. > http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like Newton's > cradle does require cross-correlation to observe, because of the intrinsic > asynchronicity, but that would require particular plasticity conditions. > > >> I suppose that it might be due to the >> relatively limited degree of freedom of the backbones (2 dihedrals >> with 3 minimum conformations) in comparison to the side-chains so the >> correlation in the backbone might be more expected. > > > Backbone atoms can only move in concert with others, yes. > > >> >> In addition as I've told you during analysis of filtered.xtc processed >> trajectory I didnt observe any fluctuations of side chains on the >> whole. > > > Yes, but the amplitude of single-side-chain motions is necessarily small, so > it doesn't follow that you should observe it in the eigenvectors with the > largest fluctuations. There's no direct connection to the energy required > for such motions, either. You should be looking at some small peptide > systems to learn how to make observations of motion you know occurs, before > trying to observe hypothesized motion. > > >>Finally I've noticed some bugs in the visualistion of the >> side-chains of the structures processed after g_covar ( e.g >> EDA_average.pdb) In that case the geometry of some side-chains (mainly >> of aromatic rings) were very distorted. Why this might occur ? > > > http://www.gromacs.org/Documentation/Terminology/Average_Structure > > Mark > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Re: Cross-correlation maps
On 28/08/2012 4:09 PM, James Starlight wrote: Mark, Thanks for explanation! 2012/8/27, Mark Abraham : Did you construct a correlation matrix from side chain atoms? Yes, and there is some degree of correlation between adjacent side chains but lack of any cooperativety between distant side-chains. In comparison in that protein there were alot of cooperativity in motion of the distinct backbones. Then that might be the conclusion, but that's your judgement to make from the full context. It's hardly likely that there'd be magical "action at a distance," but motion along the lines of Newton's cradle could have been detected and would be fascinating to see in a protein (e.g. http://www.youtube.com/watch?v=H7P4xOUPYVw). Motion exactly like Newton's cradle does require cross-correlation to observe, because of the intrinsic asynchronicity, but that would require particular plasticity conditions. I suppose that it might be due to the relatively limited degree of freedom of the backbones (2 dihedrals with 3 minimum conformations) in comparison to the side-chains so the correlation in the backbone might be more expected. Backbone atoms can only move in concert with others, yes. In addition as I've told you during analysis of filtered.xtc processed trajectory I didnt observe any fluctuations of side chains on the whole. Yes, but the amplitude of single-side-chain motions is necessarily small, so it doesn't follow that you should observe it in the eigenvectors with the largest fluctuations. There's no direct connection to the energy required for such motions, either. You should be looking at some small peptide systems to learn how to make observations of motion you know occurs, before trying to observe hypothesized motion. Finally I've noticed some bugs in the visualistion of the side-chains of the structures processed after g_covar ( e.g EDA_average.pdb) In that case the geometry of some side-chains (mainly of aromatic rings) were very distorted. Why this might occur ? http://www.gromacs.org/Documentation/Terminology/Average_Structure Mark -- 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] Re: Cross-correlation maps
Mark, Thanks for explanation! 2012/8/27, Mark Abraham : > Did you construct a correlation matrix from side chain atoms? Yes, and there is some degree of correlation between adjacent side chains but lack of any cooperativety between distant side-chains. In comparison in that protein there were alot of cooperativity in motion of the distinct backbones. I suppose that it might be due to the relatively limited degree of freedom of the backbones (2 dihedrals with 3 minimum conformations) in comparison to the side-chains so the correlation in the backbone might be more expected. In addition as I've told you during analysis of filtered.xtc processed trajectory I didnt observe any fluctuations of side chains on the whole. Finally I've noticed some bugs in the visualistion of the side-chains of the structures processed after g_covar ( e.g EDA_average.pdb) In that case the geometry of some side-chains (mainly of aromatic rings) were very distorted. Why this might occur ? -- 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] Re: Cross-correlation maps
On 28/08/2012 3:09 PM, James Starlight wrote: Hi Tsjerk! Normally during analysis of the MD trajectory I've observed frequent side-chain fluctuations (ps timescale) cased by the temperature motion of the atoms as well as larger-scale backbone motions ( on the ns time). The ps side-chains motions are known to especially increase total enthropy of the system in comparison to the backbone dynamics where such factor is less meaningful. Also there is suggestion that such enthropy-dominated motions could be functional-relevant due to possible coperativity of that process ( e.g fluctuations in one side of protein case increase dynamics in another part of such molecule without visible pathways between both parts ) So you're looking for correlated motion of atoms distant in space. That will appear as off-diagonal entries in the correlation matrix. Think about what sort of correlation matrices and eigenstructure you would expect for a system of a small number of SHM oscillators under different sorts of correlation conditions. Then worry about proteins. The main goal of my study to find out such coperativity in some proteins. So I want to detect such coperativity in fluctuations of the side-chains. As I've found the only way to do it is the calculation of the cross-correlation maps. Cross-correlation is an analysis distinct from looking at off-diagonal (a.k.a. "cross") elements of a correlation matrix. When I've performed PCA of my 100ns trajectory and examined filtered.xtc trajectory consisted of first 50 principal components) I didt observed any fluctuations of the side-chains ( only backbone motions were presented) So I could calculate only correlations in the backbone atoms motions. Is there any way to observe such cross-correlations for side chains as well ? Did you construct a correlation matrix from side chain atoms? Mark James 2012/8/27, Tsjerk Wassenaar : Hi James, Correlation is covariance normalized to variance. So you'll need the covariance matrix anyway. But what exactly due you mean with the loss of information, which you could solve with correlations? Cheers, Tsjerk On Aug 27, 2012 4:01 PM, "James Starlight" wrote: Mark, Is there any way to calculate such cross-correlations without calculation of the covariance matrix ( from the MD trajectory indirectly) ? I've noticed that after processind of my trajectory with PCA method some dynamics ( e.g fluctuations of the side-chains) are lost even when I've analysed filtered.xtc from the first 50 principal components. How I should analyse possible cross-correlations of the fluctuations of the side-chains? James 2012/8/27 Mark Abraham : On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's appeared two additional question... -- 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 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] Re: Cross-correlation maps
Hi Tsjerk! Normally during analysis of the MD trajectory I've observed frequent side-chain fluctuations (ps timescale) cased by the temperature motion of the atoms as well as larger-scale backbone motions ( on the ns time). The ps side-chains motions are known to especially increase total enthropy of the system in comparison to the backbone dynamics where such factor is less meaningful. Also there is suggestion that such enthropy-dominated motions could be functional-relevant due to possible coperativity of that process ( e.g fluctuations in one side of protein case increase dynamics in another part of such molecule without visible pathways between both parts ) The main goal of my study to find out such coperativity in some proteins. So I want to detect such coperativity in fluctuations of the side-chains. As I've found the only way to do it is the calculation of the cross-correlation maps. When I've performed PCA of my 100ns trajectory and examined filtered.xtc trajectory consisted of first 50 principal components) I didt observed any fluctuations of the side-chains ( only backbone motions were presented) So I could calculate only correlations in the backbone atoms motions. Is there any way to observe such cross-correlations for side chains as well ? James 2012/8/27, Tsjerk Wassenaar : > Hi James, > > Correlation is covariance normalized to variance. So you'll need the > covariance matrix anyway. But what exactly due you mean with the loss of > information, which you could solve with correlations? > > Cheers, > > Tsjerk > > On Aug 27, 2012 4:01 PM, "James Starlight" wrote: > > Mark, > > Is there any way to calculate such cross-correlations without > calculation of the covariance matrix ( from the MD trajectory > indirectly) ? > I've noticed that after processind of my trajectory with PCA method > some dynamics ( e.g fluctuations of the side-chains) are lost even > when I've analysed filtered.xtc from the first 50 principal > components. How I should analyse possible cross-correlations of the > fluctuations of the side-chains? > > James > > 2012/8/27 Mark Abraham : > >> On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's > appeared two additional question... > -- > 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 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] Re: Cross-correlation maps
Hi James, Correlation is covariance normalized to variance. So you'll need the covariance matrix anyway. But what exactly due you mean with the loss of information, which you could solve with correlations? Cheers, Tsjerk On Aug 27, 2012 4:01 PM, "James Starlight" wrote: Mark, Is there any way to calculate such cross-correlations without calculation of the covariance matrix ( from the MD trajectory indirectly) ? I've noticed that after processind of my trajectory with PCA method some dynamics ( e.g fluctuations of the side-chains) are lost even when I've analysed filtered.xtc from the first 50 principal components. How I should analyse possible cross-correlations of the fluctuations of the side-chains? James 2012/8/27 Mark Abraham : > On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's appeared two additional question... -- 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] Re: Cross-correlation maps
Mark, Is there any way to calculate such cross-correlations without calculation of the covariance matrix ( from the MD trajectory indirectly) ? I've noticed that after processind of my trajectory with PCA method some dynamics ( e.g fluctuations of the side-chains) are lost even when I've analysed filtered.xtc from the first 50 principal components. How I should analyse possible cross-correlations of the fluctuations of the side-chains? James 2012/8/27 Mark Abraham : > On 24/08/2012 4:51 PM, James Starlight wrote: >> >> up :) >> It's appeared two additional questions. >> >> 1) In addition to the pca's cross-correlation maps I wounder to know >> about possibility of calculation of such cross-correlation's from the >> trajectories indirectly without calculation of the covariance >> matrices. >> >> 2) is there any way to calculate degree of fluctuations of side-chains >> ( degree of torsion's dynamics) from the different trajectories and >> to compare it ? >> E.g I have one protein in two different (apo and holo) forms. I've >> calculated two trajectories for both structures and observed different >> degree of dynamics in case of each structure ( e.g fluctuations in >> case of apo form were more frequent than in case of liganded form). >> IS there any way to direct mesure and comprison of such side-chain's >> dynamics for two trajectories? > > > Yes, but not with GROMACS tools. You can generate a .tpr for use with that > old version of g_covar with an old version of grompp in a manner similar to > the way you generate one now, but there are bunch of details different. You > may not require a .tpr, of course. Look at the file types for g_covar_mod -s > in the output for -h. > > Mark > > >> >> >> James >> >> 2012/8/15, James Starlight : >>> >>> Dear Gromacs users! >>> >>> >>> I want to obtain Cross-correlation maps ( for indication of the >>> cross-correlated fluctuations of the residues). >>> The example of such maps can be found here >>> http://pubs.acs.org/doi/abs/10.1021/ja076046a >>> >>> I found that modificied version of the G_covar from users >>> contributions can do such things. But because of the older version of >>> that program (3.3.3) I've obtained the below error using it with 4.5.5 >>> gromacs >>> >>> >>> Reading file md_GO.tpr, VERSION 4.5.5 (single precision) >>> >>> --- >>> Program g_covar_mod, VERSION 3.3.3 >>> Source code file: tpxio.c, line: 1192 >>> >>> Fatal error: >>> reading tpx file (md_GO.tpr) version 73 with version 40 program >>> --- >>> >>> >>> Is there newest versions of the G_covar for such things or >>> alternativelly any others ways to calculate such correlations maps ? >>> >>> Thanks for help >>> >>> James >>> > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 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] Re: Cross-correlation maps
On 24/08/2012 4:51 PM, James Starlight wrote: up :) It's appeared two additional questions. 1) In addition to the pca's cross-correlation maps I wounder to know about possibility of calculation of such cross-correlation's from the trajectories indirectly without calculation of the covariance matrices. 2) is there any way to calculate degree of fluctuations of side-chains ( degree of torsion's dynamics) from the different trajectories and to compare it ? E.g I have one protein in two different (apo and holo) forms. I've calculated two trajectories for both structures and observed different degree of dynamics in case of each structure ( e.g fluctuations in case of apo form were more frequent than in case of liganded form). IS there any way to direct mesure and comprison of such side-chain's dynamics for two trajectories? Yes, but not with GROMACS tools. You can generate a .tpr for use with that old version of g_covar with an old version of grompp in a manner similar to the way you generate one now, but there are bunch of details different. You may not require a .tpr, of course. Look at the file types for g_covar_mod -s in the output for -h. Mark James 2012/8/15, James Starlight : Dear Gromacs users! I want to obtain Cross-correlation maps ( for indication of the cross-correlated fluctuations of the residues). The example of such maps can be found here http://pubs.acs.org/doi/abs/10.1021/ja076046a I found that modificied version of the G_covar from users contributions can do such things. But because of the older version of that program (3.3.3) I've obtained the below error using it with 4.5.5 gromacs Reading file md_GO.tpr, VERSION 4.5.5 (single precision) --- Program g_covar_mod, VERSION 3.3.3 Source code file: tpxio.c, line: 1192 Fatal error: reading tpx file (md_GO.tpr) version 73 with version 40 program --- Is there newest versions of the G_covar for such things or alternativelly any others ways to calculate such correlations maps ? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Re: Cross-correlation maps
up :) It's appeared two additional questions. 1) In addition to the pca's cross-correlation maps I wounder to know about possibility of calculation of such cross-correlation's from the trajectories indirectly without calculation of the covariance matrices. 2) is there any way to calculate degree of fluctuations of side-chains ( degree of torsion's dynamics) from the different trajectories and to compare it ? E.g I have one protein in two different (apo and holo) forms. I've calculated two trajectories for both structures and observed different degree of dynamics in case of each structure ( e.g fluctuations in case of apo form were more frequent than in case of liganded form). IS there any way to direct mesure and comprison of such side-chain's dynamics for two trajectories? James 2012/8/15, James Starlight : > Dear Gromacs users! > > > I want to obtain Cross-correlation maps ( for indication of the > cross-correlated fluctuations of the residues). > The example of such maps can be found here > http://pubs.acs.org/doi/abs/10.1021/ja076046a > > I found that modificied version of the G_covar from users > contributions can do such things. But because of the older version of > that program (3.3.3) I've obtained the below error using it with 4.5.5 > gromacs > > > Reading file md_GO.tpr, VERSION 4.5.5 (single precision) > > --- > Program g_covar_mod, VERSION 3.3.3 > Source code file: tpxio.c, line: 1192 > > Fatal error: > reading tpx file (md_GO.tpr) version 73 with version 40 program > --- > > > Is there newest versions of the G_covar for such things or > alternativelly any others ways to calculate such correlations maps ? > > Thanks for help > > James > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
