Re: [gmx-users] Bin files of g_sham
If you've done PCA, you should get an output vector anaylsis as .xvg. Aside this also breaks things into the x,y,z components for the first 8 or so vectors (so 4 line graphs of energy versus time including the total energy), along with 2D plots you can generate. You would then already have what you need from that, corresponding to total energy, or total energy in an x-y plain. The timeframes would then be in those files, and you could use one of the three or so scripts in gromacs to output a .pdb for the particular frame(s) you wish. If your PCA did not generate those files in the process, you could just re-do it quickly and tell it to output those. Little brain? Your doing statistical quantum/molecular computer physics...and I alsways have my foot in my mouth on this board... xmgrace helps with figuring out the outputs (as they are all formated for this, and thus you can quickly just open them and see whats being output as well which helps in understanding them). Sincerely, Stephan Watkins Gesendet: Donnerstag, 19. Dezember 2013 um 08:39 Uhr Von: "Ankita Naithani" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Bin files of g_sham Hi Llyod, Thank you very much indeed for your kind involvement in answering my question. Yes, I did tell g_sham not expect the time while I issued the command to run it. Yes, I have done PCA already on my trajectory, could you just guide me a little further as to what is the technique which can help me to look at the frames corresponding to the the energy? Meanwhile, I shall also try to grasp your advice/suggestions and see how far can I make my little brain work towards it. Kind regards, Ankita On Thu, Dec 19, 2013 at 2:49 AM, lloyd riggs wrote: > Trying to help I would say I am trying to remember some things I did some > time ago. That said, your missing the time column as your first input. > You are making a 2D energy plot is what your telling it to do, you can also > tell it not to expect a time which would be correct for your case, however > this is a landscape your generating. It is already a total energy > landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the > boltzman inversion equation in the g_sham to break it down into gibbs, enth > and entro as .xpm plots. Your bins are the "pixels" or points in the > landscape I believe, thus the binwidth is the xmin and max, but I amnot > 100% sure how the numbering goes. You can check it against the image file > generated (look at it with gedit, the pixel portion will tell you). > > One way to get it to work, would be to supply a free energy single column > (or time, then single energy column), however someone might correct me on > this (I hope) if I am wrong. > > However your origional question was to look up or coordinate a line graph > gibbs energy plot, with a frame in your trajectory. Thus I believe you > want to look at a linear plot of your energy change over time. If you > generated the eigen vectors already, there are methods in these techniques > to look at frames versus energy (total). You can also if you designed your > experiment as a pulled/steered free energy experiment, use the g_wham, with > no bootstraping or autocorrelation, etc...with one trajectory, and it is a > sham. Otherwise, your using the wrong things to get what you want (g_ > scripts in gromacs), and need to read the manual again. You can, with an > index for only what you want, extract total energy and plot it as well > versus frame, which might give you what you want also...using just g_energy. > > I hope that helps, > > Stephan Watkins > *Gesendet:* Donnerstag, 19. Dezember 2013 um 00:09 Uhr > *Von:* jkrie...@mrc-lmb.cam.ac.uk > *An:* "gmx-us...@gromacs.org" > *Betreff:* Re: [gmx-users] Bin files of g_sham > You're not asking it to read the bin index file in your command. Maybe > that explains what you're seeing? > > On 18 Dec 2013, at 13:51, Ankita Naithani > wrote: > > > Hi Lloyd, > > > > So, my input to g_sham is a file with following lines: > > > > @ title "2D projection of trajectory" > > @ xaxis label "projection on eigenvector 1 (nm)" > > @ yaxis label "projection on eigenvector 2 (nm)" > > @TYPE xy > > 0.16750 0.18278 > > -0.01448 -0.14834 > > -0.32757 0.22259 > > -0.33832 0.63817 > > > > This file is named AM_12.xvg > > > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm > > > > My bin index file has the following lines: > > > > [ 18 ] > > 7105 > > [ 19 ] > > 7104 > > [ 46 ] > > 7124 > > [ 48 ] > > 7123 > > [ 49 ] > > 7106 > > [ 50 ] > > 6497 > > 6498 > > [
Re: [gmx-users] Bin files of g_sham
Since you already built 2-d free energy landscape (FEL), you should have PCs (PC1 and PC2) as a function of time. You also know from the minima of FEL at which PCs the system spends longer time. Once you find those PCs you should find when the system has those PCs (from PC vs time). Then you should visualize your trajectory and check the structures at those periods of time. Once you collect all the structures you can pick the representative structure. On Thu, Dec 19, 2013 at 1:09 PM, Ankita Naithani wrote: > Hi Llyod, > > Thank you very much indeed for your kind involvement in answering my > question. Yes, I did tell g_sham not expect the time while I issued the > command to run it. Yes, I have done PCA already on my trajectory, could you > just guide me a little further as to what is the technique which can help > me to look at the frames corresponding to the the energy? Meanwhile, I > shall also try to grasp your advice/suggestions and see how far can I make > my little brain work towards it. > > Kind regards, > > Ankita > > > On Thu, Dec 19, 2013 at 2:49 AM, lloyd riggs wrote: > > > Trying to help I would say I am trying to remember some things I did some > > time ago. That said, your missing the time column as your first input. > > You are making a 2D energy plot is what your telling it to do, you can > also > > tell it not to expect a time which would be correct for your case, > however > > this is a landscape your generating. It is already a total energy > > landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the > > boltzman inversion equation in the g_sham to break it down into gibbs, > enth > > and entro as .xpm plots. Your bins are the "pixels" or points in the > > landscape I believe, thus the binwidth is the xmin and max, but I amnot > > 100% sure how the numbering goes. You can check it against the image file > > generated (look at it with gedit, the pixel portion will tell you). > > > > One way to get it to work, would be to supply a free energy single column > > (or time, then single energy column), however someone might correct me > on > > this (I hope) if I am wrong. > > > > However your origional question was to look up or coordinate a line graph > > gibbs energy plot, with a frame in your trajectory. Thus I believe you > > want to look at a linear plot of your energy change over time. If you > > generated the eigen vectors already, there are methods in these > techniques > > to look at frames versus energy (total). You can also if you designed > your > > experiment as a pulled/steered free energy experiment, use the g_wham, > with > > no bootstraping or autocorrelation, etc...with one trajectory, and it is > a > > sham. Otherwise, your using the wrong things to get what you want (g_ > > scripts in gromacs), and need to read the manual again. You can, with an > > index for only what you want, extract total energy and plot it as well > > versus frame, which might give you what you want also...using just > g_energy. > > > > I hope that helps, > > > > Stephan Watkins > > *Gesendet:* Donnerstag, 19. Dezember 2013 um 00:09 Uhr > > *Von:* jkrie...@mrc-lmb.cam.ac.uk > > *An:* "gmx-us...@gromacs.org" > > *Betreff:* Re: [gmx-users] Bin files of g_sham > > You're not asking it to read the bin index file in your command. Maybe > > that explains what you're seeing? > > > > On 18 Dec 2013, at 13:51, Ankita Naithani > > wrote: > > > > > Hi Lloyd, > > > > > > So, my input to g_sham is a file with following lines: > > > > > > @ title "2D projection of trajectory" > > > @ xaxis label "projection on eigenvector 1 (nm)" > > > @ yaxis label "projection on eigenvector 2 (nm)" > > > @TYPE xy > > > 0.16750 0.18278 > > > -0.01448 -0.14834 > > > -0.32757 0.22259 > > > -0.33832 0.63817 > > > > > > This file is named AM_12.xvg > > > > > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm > > > > > > My bin index file has the following lines: > > > > > > [ 18 ] > > > 7105 > > > [ 19 ] > > > 7104 > > > [ 46 ] > > > 7124 > > > [ 48 ] > > > 7123 > > > [ 49 ] > > > 7106 > > > [ 50 ] > > > 6497 > > > 6498 > > > [ 51 ] > > > 6499 > > > 6500 > > > [ 52 ] > > > 6496 > > > 7103 > > > [ 53 ] > > > 7102 > > > [ 55 ] > > > 6672 >
Re: [gmx-users] Bin files of g_sham
Hi Llyod, Thank you very much indeed for your kind involvement in answering my question. Yes, I did tell g_sham not expect the time while I issued the command to run it. Yes, I have done PCA already on my trajectory, could you just guide me a little further as to what is the technique which can help me to look at the frames corresponding to the the energy? Meanwhile, I shall also try to grasp your advice/suggestions and see how far can I make my little brain work towards it. Kind regards, Ankita On Thu, Dec 19, 2013 at 2:49 AM, lloyd riggs wrote: > Trying to help I would say I am trying to remember some things I did some > time ago. That said, your missing the time column as your first input. > You are making a 2D energy plot is what your telling it to do, you can also > tell it not to expect a time which would be correct for your case, however > this is a landscape your generating. It is already a total energy > landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the > boltzman inversion equation in the g_sham to break it down into gibbs, enth > and entro as .xpm plots. Your bins are the "pixels" or points in the > landscape I believe, thus the binwidth is the xmin and max, but I amnot > 100% sure how the numbering goes. You can check it against the image file > generated (look at it with gedit, the pixel portion will tell you). > > One way to get it to work, would be to supply a free energy single column > (or time, then single energy column), however someone might correct me on > this (I hope) if I am wrong. > > However your origional question was to look up or coordinate a line graph > gibbs energy plot, with a frame in your trajectory. Thus I believe you > want to look at a linear plot of your energy change over time. If you > generated the eigen vectors already, there are methods in these techniques > to look at frames versus energy (total). You can also if you designed your > experiment as a pulled/steered free energy experiment, use the g_wham, with > no bootstraping or autocorrelation, etc...with one trajectory, and it is a > sham. Otherwise, your using the wrong things to get what you want (g_ > scripts in gromacs), and need to read the manual again. You can, with an > index for only what you want, extract total energy and plot it as well > versus frame, which might give you what you want also...using just g_energy. > > I hope that helps, > > Stephan Watkins > *Gesendet:* Donnerstag, 19. Dezember 2013 um 00:09 Uhr > *Von:* jkrie...@mrc-lmb.cam.ac.uk > *An:* "gmx-us...@gromacs.org" > *Betreff:* Re: [gmx-users] Bin files of g_sham > You're not asking it to read the bin index file in your command. Maybe > that explains what you're seeing? > > On 18 Dec 2013, at 13:51, Ankita Naithani > wrote: > > > Hi Lloyd, > > > > So, my input to g_sham is a file with following lines: > > > > @ title "2D projection of trajectory" > > @ xaxis label "projection on eigenvector 1 (nm)" > > @ yaxis label "projection on eigenvector 2 (nm)" > > @TYPE xy > > 0.16750 0.18278 > > -0.01448 -0.14834 > > -0.32757 0.22259 > > -0.33832 0.63817 > > > > This file is named AM_12.xvg > > > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm > > > > My bin index file has the following lines: > > > > [ 18 ] > > 7105 > > [ 19 ] > > 7104 > > [ 46 ] > > 7124 > > [ 48 ] > > 7123 > > [ 49 ] > > 7106 > > [ 50 ] > > 6497 > > 6498 > > [ 51 ] > > 6499 > > 6500 > > [ 52 ] > > 6496 > > 7103 > > [ 53 ] > > 7102 > > [ 55 ] > > 6672 > > [ 75 ] > > 5745 > > 5749 > > and so on. > > > > I am not sure how can I look at the default binwidth. > > > > Kind regards, > > > > Ankita > > > > > > On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs wrote: > > > >> > >> You need to explain what you are doing better, what you want to do, and > >> show your input (command line, .xvg lines of input and output as > example) > >> and you might get more help on here. If you read the -h from g_sham, it > is > >> making a single plot from your input, and in this case your .xpm would > be a > >> matrix with bins on a 2D surface with points taken across the entire > run, > >> as an example of what I mean. I believe you can also use a single line > >> (time, energy as column 2), and get a single line out as well, with a > >> meaningless "landscape" still put out as .xpm, etc...look at your > binwidth > >> d
Re: [gmx-users] Bin files of g_sham
Trying to help I would say I am trying to remember some things I did some time ago. That said, your missing the time column as your first input. You are making a 2D energy plot is what your telling it to do, you can also tell it not to expect a time which would be correct for your case, however this is a landscape your generating. It is already a total energy landscape in 1 nm by 2 nm 2D volumn, what your doing is trying to use the boltzman inversion equation in the g_sham to break it down into gibbs, enth and entro as .xpm plots. Your bins are the "pixels" or points in the landscape I believe, thus the binwidth is the xmin and max, but I amnot 100% sure how the numbering goes. You can check it against the image file generated (look at it with gedit, the pixel portion will tell you). One way to get it to work, would be to supply a free energy single column (or time, then single energy column), however someone might correct me on this (I hope) if I am wrong. However your origional question was to look up or coordinate a line graph gibbs energy plot, with a frame in your trajectory. Thus I believe you want to look at a linear plot of your energy change over time. If you generated the eigen vectors already, there are methods in these techniques to look at frames versus energy (total). You can also if you designed your experiment as a pulled/steered free energy experiment, use the g_wham, with no bootstraping or autocorrelation, etc...with one trajectory, and it is a sham. Otherwise, your using the wrong things to get what you want (g_ scripts in gromacs), and need to read the manual again. You can, with an index for only what you want, extract total energy and plot it as well versus frame, which might give you what you want also...using just g_energy. I hope that helps, Stephan Watkins Gesendet: Donnerstag, 19. Dezember 2013 um 00:09 Uhr Von: jkrie...@mrc-lmb.cam.ac.uk An: "gmx-us...@gromacs.org" Betreff: Re: [gmx-users] Bin files of g_sham You're not asking it to read the bin index file in your command. Maybe that explains what you're seeing? On 18 Dec 2013, at 13:51, Ankita Naithani wrote: > Hi Lloyd, > > So, my input to g_sham is a file with following lines: > > @ title "2D projection of trajectory" > @ xaxis label "projection on eigenvector 1 (nm)" > @ yaxis label "projection on eigenvector 2 (nm)" > @TYPE xy > 0.16750 0.18278 > -0.01448 -0.14834 > -0.32757 0.22259 > -0.33832 0.63817 > > This file is named AM_12.xvg > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm > > My bin index file has the following lines: > > [ 18 ] > 7105 > [ 19 ] > 7104 > [ 46 ] > 7124 > [ 48 ] > 7123 > [ 49 ] > 7106 > [ 50 ] > 6497 > 6498 > [ 51 ] > 6499 > 6500 > [ 52 ] > 6496 > 7103 > [ 53 ] > 7102 > [ 55 ] > 6672 > [ 75 ] > 5745 > 5749 > and so on. > > I am not sure how can I look at the default binwidth. > > Kind regards, > > Ankita > > > On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs wrote: > >> >> You need to explain what you are doing better, what you want to do, and >> show your input (command line, .xvg lines of input and output as example) >> and you might get more help on here. If you read the -h from g_sham, it is >> making a single plot from your input, and in this case your .xpm would be a >> matrix with bins on a 2D surface with points taken across the entire run, >> as an example of what I mean. I believe you can also use a single line >> (time, energy as column 2), and get a single line out as well, with a >> meaningless "landscape" still put out as .xpm, etc...look at your binwidth >> default, input and what you want out is all I could say at this point. You >> might be trying to do something else however... >> >> Stephan >> *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr >> >> *Von:* "Ankita Naithani" >> *An:* "Discussion list for GROMACS users" >> *Betreff:* Re: [gmx-users] Bin files of g_sham >> I would like to add that maybe the bins store Frame numbers. Because I seem >> to have around 21000 frames and I guess I am unable to see a number higher >> than that. Apologies for the confusion about earlier number. So, in this >> case if I want a confirmation at a particular frame number, how should I go >> about that? Could you please help me with that? >> >> Kind regards, >> >> Ankita >> >> >> On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani >> wrote: >> >>> Hi Llyod, >>> >>> Thank you for your reply. I actually wanted to extract frames >>> corresponding to the g_sham output. T
Re: [gmx-users] Bin files of g_sham
You're not asking it to read the bin index file in your command. Maybe that explains what you're seeing? On 18 Dec 2013, at 13:51, Ankita Naithani wrote: > Hi Lloyd, > > So, my input to g_sham is a file with following lines: > > @title "2D projection of trajectory" > @xaxis label "projection on eigenvector 1 (nm)" > @yaxis label "projection on eigenvector 2 (nm)" > @TYPE xy > 0.167500.18278 > -0.01448 -0.14834 > -0.327570.22259 > -0.338320.63817 > > This file is named AM_12.xvg > > and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm > > My bin index file has the following lines: > > [ 18 ] > 7105 > [ 19 ] > 7104 > [ 46 ] > 7124 > [ 48 ] > 7123 > [ 49 ] > 7106 > [ 50 ] > 6497 > 6498 > [ 51 ] > 6499 > 6500 > [ 52 ] > 6496 > 7103 > [ 53 ] > 7102 > [ 55 ] > 6672 > [ 75 ] > 5745 > 5749 > and so on. > > I am not sure how can I look at the default binwidth. > > Kind regards, > > Ankita > > > On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs wrote: > >> >> You need to explain what you are doing better, what you want to do, and >> show your input (command line, .xvg lines of input and output as example) >> and you might get more help on here. If you read the -h from g_sham, it is >> making a single plot from your input, and in this case your .xpm would be a >> matrix with bins on a 2D surface with points taken across the entire run, >> as an example of what I mean. I believe you can also use a single line >> (time, energy as column 2), and get a single line out as well, with a >> meaningless "landscape" still put out as .xpm, etc...look at your binwidth >> default, input and what you want out is all I could say at this point. You >> might be trying to do something else however... >> >> Stephan >> *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr >> >> *Von:* "Ankita Naithani" >> *An:* "Discussion list for GROMACS users" >> *Betreff:* Re: [gmx-users] Bin files of g_sham >> I would like to add that maybe the bins store Frame numbers. Because I seem >> to have around 21000 frames and I guess I am unable to see a number higher >> than that. Apologies for the confusion about earlier number. So, in this >> case if I want a confirmation at a particular frame number, how should I go >> about that? Could you please help me with that? >> >> Kind regards, >> >> Ankita >> >> >> On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani >> wrote: >> >>> Hi Llyod, >>> >>> Thank you for your reply. I actually wanted to extract frames >>> corresponding to the g_sham output. The input for g_sham in my case was >>> column 1 had time points, column 2 and column 3 had Principal component 1 >>> and Principal component 2 respectively. So, the binning which has been >>> done, i.e. if I say that the bin number 786 has the following few numbers >>> like : 3876, 9870, 22002 etc. These should technically correspond to the >>> time points right which I can then dump using trjconv too maybe. >>> >>> Also, I am a little confused because if the bins have all the time >> points, >>> I don't seem to find the time points uptil the end of simulation in that >>> case i.e. I am unable to see higher time scale. My simulation was for >> 48ns >>> and had 3fs time step. I am unable to trace anything beyond 22000 or >> 23000 >>> number in my bins. >>> >>> I hope you could help me solve this confusion. >>> >>> Kind regards, >>> >>> Ankita >>> >>> >>> On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs >> wrote: >>> >>>> >>>> I will attempt an answer, however there might be a better response. It >>>> depends on your input .xvg (what the first column is) and what you are >>>> telling it to do (defualt is time), and if these correspond to your time >>>> frames (can be timepoint or siply frame # I believe). g_sham seems (to >> me) >>>> to work like a comand line spread sheet manipulator with some built in >>>> functions. If you want a particular frame from a trajectory time point, >>>> then use g_traj with the first/last set to the frame you want but >> there's >>>> also 2 other tools that do this the same way... >>>> >>>> Stephan Watkins >>>> *Gesendet:* Sonntag,
Re: [gmx-users] Bin files of g_sham
Hi Lloyd, So, my input to g_sham is a file with following lines: @title "2D projection of trajectory" @xaxis label "projection on eigenvector 1 (nm)" @yaxis label "projection on eigenvector 2 (nm)" @TYPE xy 0.167500.18278 -0.01448 -0.14834 -0.327570.22259 -0.338320.63817 This file is named AM_12.xvg and my command line is g_sham -f AM_12.xvg -ls AM_FEL_12.xpm My bin index file has the following lines: [ 18 ] 7105 [ 19 ] 7104 [ 46 ] 7124 [ 48 ] 7123 [ 49 ] 7106 [ 50 ] 6497 6498 [ 51 ] 6499 6500 [ 52 ] 6496 7103 [ 53 ] 7102 [ 55 ] 6672 [ 75 ] 5745 5749 and so on. I am not sure how can I look at the default binwidth. Kind regards, Ankita On Tue, Dec 17, 2013 at 6:03 PM, lloyd riggs wrote: > > You need to explain what you are doing better, what you want to do, and > show your input (command line, .xvg lines of input and output as example) > and you might get more help on here. If you read the -h from g_sham, it is > making a single plot from your input, and in this case your .xpm would be a > matrix with bins on a 2D surface with points taken across the entire run, > as an example of what I mean. I believe you can also use a single line > (time, energy as column 2), and get a single line out as well, with a > meaningless "landscape" still put out as .xpm, etc...look at your binwidth > default, input and what you want out is all I could say at this point. You > might be trying to do something else however... > > Stephan > *Gesendet:* Dienstag, 17. Dezember 2013 um 08:38 Uhr > > *Von:* "Ankita Naithani" > *An:* "Discussion list for GROMACS users" > *Betreff:* Re: [gmx-users] Bin files of g_sham > I would like to add that maybe the bins store Frame numbers. Because I seem > to have around 21000 frames and I guess I am unable to see a number higher > than that. Apologies for the confusion about earlier number. So, in this > case if I want a confirmation at a particular frame number, how should I go > about that? Could you please help me with that? > > Kind regards, > > Ankita > > > On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani > wrote: > > > Hi Llyod, > > > > Thank you for your reply. I actually wanted to extract frames > > corresponding to the g_sham output. The input for g_sham in my case was > > column 1 had time points, column 2 and column 3 had Principal component 1 > > and Principal component 2 respectively. So, the binning which has been > > done, i.e. if I say that the bin number 786 has the following few numbers > > like : 3876, 9870, 22002 etc. These should technically correspond to the > > time points right which I can then dump using trjconv too maybe. > > > > Also, I am a little confused because if the bins have all the time > points, > > I don't seem to find the time points uptil the end of simulation in that > > case i.e. I am unable to see higher time scale. My simulation was for > 48ns > > and had 3fs time step. I am unable to trace anything beyond 22000 or > 23000 > > number in my bins. > > > > I hope you could help me solve this confusion. > > > > Kind regards, > > > > Ankita > > > > > > On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs > wrote: > > > >> > >> I will attempt an answer, however there might be a better response. It > >> depends on your input .xvg (what the first column is) and what you are > >> telling it to do (defualt is time), and if these correspond to your time > >> frames (can be timepoint or siply frame # I believe). g_sham seems (to > me) > >> to work like a comand line spread sheet manipulator with some built in > >> functions. If you want a particular frame from a trajectory time point, > >> then use g_traj with the first/last set to the frame you want but > there's > >> also 2 other tools that do this the same way... > >> > >> Stephan Watkins > >> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr > >> *Von:* "Ankita Naithani" > >> *An:* "Discussion list for GROMACS users" > >> *Betreff:* [gmx-users] Bin files of g_sham > > >> Hi, > >> > >> I had a query regarding the bin files generated by g_sham. > >> Does the bin index contain timepoints? i.e. there are 1024 bins so each > >> bin > >> has a number of time points? And supposes bin 756 has numbers like 3876, > >> 20020, 7896 so these would all correspond to time and we could then dump > >> the representative frame corresponding to these time points? > >> > >> I am a little confused as to wh
Re: [gmx-users] Bin files of g_sham
You need to explain what you are doing better, what you want to do, and show your input (command line, .xvg lines of input and output as example) and you might get more help on here. If you read the -h from g_sham, it is making a single plot from your input, and in this case your .xpm would be a matrix with bins on a 2D surface with points taken across the entire run, as an example of what I mean. I believe you can also use a single line (time, energy as column 2), and get a single line out as well, with a meaningless "landscape" still put out as .xpm, etc...look at your binwidth default, input and what you want out is all I could say at this point. You might be trying to do something else however... Stephan Gesendet: Dienstag, 17. Dezember 2013 um 08:38 Uhr Von: "Ankita Naithani" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Bin files of g_sham I would like to add that maybe the bins store Frame numbers. Because I seem to have around 21000 frames and I guess I am unable to see a number higher than that. Apologies for the confusion about earlier number. So, in this case if I want a confirmation at a particular frame number, how should I go about that? Could you please help me with that? Kind regards, Ankita On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani wrote: > Hi Llyod, > > Thank you for your reply. I actually wanted to extract frames > corresponding to the g_sham output. The input for g_sham in my case was > column 1 had time points, column 2 and column 3 had Principal component 1 > and Principal component 2 respectively. So, the binning which has been > done, i.e. if I say that the bin number 786 has the following few numbers > like : 3876, 9870, 22002 etc. These should technically correspond to the > time points right which I can then dump using trjconv too maybe. > > Also, I am a little confused because if the bins have all the time points, > I don't seem to find the time points uptil the end of simulation in that > case i.e. I am unable to see higher time scale. My simulation was for 48ns > and had 3fs time step. I am unable to trace anything beyond 22000 or 23000 > number in my bins. > > I hope you could help me solve this confusion. > > Kind regards, > > Ankita > > > On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs wrote: > >> >> I will attempt an answer, however there might be a better response. It >> depends on your input .xvg (what the first column is) and what you are >> telling it to do (defualt is time), and if these correspond to your time >> frames (can be timepoint or siply frame # I believe). g_sham seems (to me) >> to work like a comand line spread sheet manipulator with some built in >> functions. If you want a particular frame from a trajectory time point, >> then use g_traj with the first/last set to the frame you want but there's >> also 2 other tools that do this the same way... >> >> Stephan Watkins >> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr >> *Von:* "Ankita Naithani" >> *An:* "Discussion list for GROMACS users" >> *Betreff:* [gmx-users] Bin files of g_sham >> Hi, >> >> I had a query regarding the bin files generated by g_sham. >> Does the bin index contain timepoints? i.e. there are 1024 bins so each >> bin >> has a number of time points? And supposes bin 756 has numbers like 3876, >> 20020, 7896 so these would all correspond to time and we could then dump >> the representative frame corresponding to these time points? >> >> I am a little confused as to what is stored in the bins? Timepoints or >> frame number and then alternatively how to get the representative >> frame/snapshot stored at that specific bin number. >> >> Kind regards, >> >> -- >> Ankita Naithani >> -- >> 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] Bin files of g_sham
I would like to add that maybe the bins store Frame numbers. Because I seem to have around 21000 frames and I guess I am unable to see a number higher than that. Apologies for the confusion about earlier number. So, in this case if I want a confirmation at a particular frame number, how should I go about that? Could you please help me with that? Kind regards, Ankita On Tue, Dec 17, 2013 at 7:20 AM, Ankita Naithani wrote: > Hi Llyod, > > Thank you for your reply. I actually wanted to extract frames > corresponding to the g_sham output. The input for g_sham in my case was > column 1 had time points, column 2 and column 3 had Principal component 1 > and Principal component 2 respectively. So, the binning which has been > done, i.e. if I say that the bin number 786 has the following few numbers > like : 3876, 9870, 22002 etc. These should technically correspond to the > time points right which I can then dump using trjconv too maybe. > > Also, I am a little confused because if the bins have all the time points, > I don't seem to find the time points uptil the end of simulation in that > case i.e. I am unable to see higher time scale. My simulation was for 48ns > and had 3fs time step. I am unable to trace anything beyond 22000 or 23000 > number in my bins. > > I hope you could help me solve this confusion. > > Kind regards, > > Ankita > > > On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs wrote: > >> >> I will attempt an answer, however there might be a better response. It >> depends on your input .xvg (what the first column is) and what you are >> telling it to do (defualt is time), and if these correspond to your time >> frames (can be timepoint or siply frame # I believe). g_sham seems (to me) >> to work like a comand line spread sheet manipulator with some built in >> functions. If you want a particular frame from a trajectory time point, >> then use g_traj with the first/last set to the frame you want but there's >> also 2 other tools that do this the same way... >> >> Stephan Watkins >> *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr >> *Von:* "Ankita Naithani" >> *An:* "Discussion list for GROMACS users" >> *Betreff:* [gmx-users] Bin files of g_sham >> Hi, >> >> I had a query regarding the bin files generated by g_sham. >> Does the bin index contain timepoints? i.e. there are 1024 bins so each >> bin >> has a number of time points? And supposes bin 756 has numbers like 3876, >> 20020, 7896 so these would all correspond to time and we could then dump >> the representative frame corresponding to these time points? >> >> I am a little confused as to what is stored in the bins? Timepoints or >> frame number and then alternatively how to get the representative >> frame/snapshot stored at that specific bin number. >> >> Kind regards, >> >> -- >> Ankita Naithani >> -- >> 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. >> >> > > > -- > Ankita Naithani > -- Ankita Naithani -- 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] Bin files of g_sham
Hi Llyod, Thank you for your reply. I actually wanted to extract frames corresponding to the g_sham output. The input for g_sham in my case was column 1 had time points, column 2 and column 3 had Principal component 1 and Principal component 2 respectively. So, the binning which has been done, i.e. if I say that the bin number 786 has the following few numbers like : 3876, 9870, 22002 etc. These should technically correspond to the time points right which I can then dump using trjconv too maybe. Also, I am a little confused because if the bins have all the time points, I don't seem to find the time points uptil the end of simulation in that case i.e. I am unable to see higher time scale. My simulation was for 48ns and had 3fs time step. I am unable to trace anything beyond 22000 or 23000 number in my bins. I hope you could help me solve this confusion. Kind regards, Ankita On Sun, Dec 15, 2013 at 11:17 PM, lloyd riggs wrote: > > I will attempt an answer, however there might be a better response. It > depends on your input .xvg (what the first column is) and what you are > telling it to do (defualt is time), and if these correspond to your time > frames (can be timepoint or siply frame # I believe). g_sham seems (to me) > to work like a comand line spread sheet manipulator with some built in > functions. If you want a particular frame from a trajectory time point, > then use g_traj with the first/last set to the frame you want but there's > also 2 other tools that do this the same way... > > Stephan Watkins > *Gesendet:* Sonntag, 15. Dezember 2013 um 14:49 Uhr > *Von:* "Ankita Naithani" > *An:* "Discussion list for GROMACS users" > *Betreff:* [gmx-users] Bin files of g_sham > Hi, > > I had a query regarding the bin files generated by g_sham. > Does the bin index contain timepoints? i.e. there are 1024 bins so each bin > has a number of time points? And supposes bin 756 has numbers like 3876, > 20020, 7896 so these would all correspond to time and we could then dump > the representative frame corresponding to these time points? > > I am a little confused as to what is stored in the bins? Timepoints or > frame number and then alternatively how to get the representative > frame/snapshot stored at that specific bin number. > > Kind regards, > > -- > Ankita Naithani > -- > 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. > > -- Ankita Naithani -- 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] Bin files of g_sham
I will attempt an answer, however there might be a better response. It depends on your input .xvg (what the first column is) and what you are telling it to do (defualt is time), and if these correspond to your time frames (can be timepoint or siply frame # I believe). g_sham seems (to me) to work like a comand line spread sheet manipulator with some built in functions. If you want a particular frame from a trajectory time point, then use g_traj with the first/last set to the frame you want but there's also 2 other tools that do this the same way... Stephan Watkins Gesendet: Sonntag, 15. Dezember 2013 um 14:49 Uhr Von: "Ankita Naithani" An: "Discussion list for GROMACS users" Betreff: [gmx-users] Bin files of g_sham Hi, I had a query regarding the bin files generated by g_sham. Does the bin index contain timepoints? i.e. there are 1024 bins so each bin has a number of time points? And supposes bin 756 has numbers like 3876, 20020, 7896 so these would all correspond to time and we could then dump the representative frame corresponding to these time points? I am a little confused as to what is stored in the bins? Timepoints or frame number and then alternatively how to get the representative frame/snapshot stored at that specific bin number. Kind regards, -- Ankita Naithani -- 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.
[gmx-users] Bin files of g_sham
Hi, I had a query regarding the bin files generated by g_sham. Does the bin index contain timepoints? i.e. there are 1024 bins so each bin has a number of time points? And supposes bin 756 has numbers like 3876, 20020, 7896 so these would all correspond to time and we could then dump the representative frame corresponding to these time points? I am a little confused as to what is stored in the bins? Timepoints or frame number and then alternatively how to get the representative frame/snapshot stored at that specific bin number. Kind regards, -- Ankita Naithani -- 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.
