Re: [gmx-users] Fwd: Help on the vector component
Hi Tsjerk, Thanks for the explanation. Yes, so basically, if I am using calpha atoms for two systems namely apo and holo (the structure is same with holo having one extra ligand from apo) and then comparing their eigenvectors, it will be a sensible comparison? Also, since these components correspond to the direction of motion associated with a particular eigenvector, will we be sensible in commenting/discussing about the collapse or emergence of eigenvector components between the two trajectories with regards to the atom position on x axis as outputted? For instance, if in Apo a particular atom has high value of total component but maybe in holo that might have a lower value, so could we try to analyse it in a component way by commenting upon the collapse or appearance of motion? [I might have been extremely confusing here, apologies for that] Kind regards, Ankita On Mon, Nov 25, 2013 at 6:45 AM, Tsjerk Wassenaar wrote: > Hi Ankita, > > If x, y, z are the components (or loadings), then "total" is sqrt(x**2 + > y**2 + z**2). They indeed define a direction, corresponding with the > direction of motion/spread associated with the eigenvector. > > To compare eigenvectors, make sure that all frames in all trajectories are > oriented in the same way, using the same or a similar reference structure > for fitting. Then you can make a comparison like that. > > Cheers, > > Tsjerk > > > On Mon, Nov 25, 2013 at 1:00 AM, Ankita Naithani > wrote: > > > Hi Tsjerk, > > > > Thank you for your reply. So, basically the numbers are just the xyz > > components. and the Total is, I quite didn't understand what the total > > would be? If they are dimensionless, does that mean they are defining a > > direction? I mean should we say that the total component for instance is > a > > measure of the direction of the eigenvector? Also, I was wondering if > this > > could be valid to use for comparison between eigenvectors of different > > trajectories to account for or observe the similarity/dissimilarity > amongst > > the two? > > > > > > Kind regards, > > > > Ankita > > > > > > On Sun, Nov 24, 2013 at 8:27 PM, Tsjerk Wassenaar > > wrote: > > > > > Hi Ankita, > > > > > > I had to check the source for this, but -comp writes out the > eigenvector > > as > > > atom-coordinate components (x,y,z), and the norm of the eigenvector > part > > of > > > the given atom (total). The numbers are dimensionless. > > > > > > Hope it helps, > > > > > > Tsjerk > > > > > > > > > On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani > > > wrote: > > > > > > > Hi, > > > > > > > > I wanted some help regarding vector components. I.e. when we use the > > > > g_anaeig command with a flag of -comp, it outputs a file of the > > > > corresponding eigenvector per atom. So, the x-axis has the atom > number > > > and > > > > the Y-axis has the total, x, y and z components. I am not sure about > > what > > > > do they mean? Also, what are the units of these components? Like the > > > > numbers on Y-axis, what are the corresponding units? I would be > really > > > > grateful if anyone could kindly help me on this. > > > > Apologies for reposting but was wondering if anyone has any thoughts > on > > > it? > > > > > > > > Best wishes, > > > > > > > > -- > > > > 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-usersor > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > Tsjerk A. Wassenaar, Ph.D. > > > -- > > > 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. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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)su
Re: [gmx-users] Fwd: Help on the vector component
Hi Ankita, If x, y, z are the components (or loadings), then "total" is sqrt(x**2 + y**2 + z**2). They indeed define a direction, corresponding with the direction of motion/spread associated with the eigenvector. To compare eigenvectors, make sure that all frames in all trajectories are oriented in the same way, using the same or a similar reference structure for fitting. Then you can make a comparison like that. Cheers, Tsjerk On Mon, Nov 25, 2013 at 1:00 AM, Ankita Naithani wrote: > Hi Tsjerk, > > Thank you for your reply. So, basically the numbers are just the xyz > components. and the Total is, I quite didn't understand what the total > would be? If they are dimensionless, does that mean they are defining a > direction? I mean should we say that the total component for instance is a > measure of the direction of the eigenvector? Also, I was wondering if this > could be valid to use for comparison between eigenvectors of different > trajectories to account for or observe the similarity/dissimilarity amongst > the two? > > > Kind regards, > > Ankita > > > On Sun, Nov 24, 2013 at 8:27 PM, Tsjerk Wassenaar > wrote: > > > Hi Ankita, > > > > I had to check the source for this, but -comp writes out the eigenvector > as > > atom-coordinate components (x,y,z), and the norm of the eigenvector part > of > > the given atom (total). The numbers are dimensionless. > > > > Hope it helps, > > > > Tsjerk > > > > > > On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani > > wrote: > > > > > Hi, > > > > > > I wanted some help regarding vector components. I.e. when we use the > > > g_anaeig command with a flag of -comp, it outputs a file of the > > > corresponding eigenvector per atom. So, the x-axis has the atom number > > and > > > the Y-axis has the total, x, y and z components. I am not sure about > what > > > do they mean? Also, what are the units of these components? Like the > > > numbers on Y-axis, what are the corresponding units? I would be really > > > grateful if anyone could kindly help me on this. > > > Apologies for reposting but was wondering if anyone has any thoughts on > > it? > > > > > > Best wishes, > > > > > > -- > > > 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. > > > > > > > > > > > -- > > Tsjerk A. Wassenaar, Ph.D. > > -- > > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] Fwd: Help on the vector component
Hi Tsjerk, Thank you for your reply. So, basically the numbers are just the xyz components. and the Total is, I quite didn't understand what the total would be? If they are dimensionless, does that mean they are defining a direction? I mean should we say that the total component for instance is a measure of the direction of the eigenvector? Also, I was wondering if this could be valid to use for comparison between eigenvectors of different trajectories to account for or observe the similarity/dissimilarity amongst the two? Kind regards, Ankita On Sun, Nov 24, 2013 at 8:27 PM, Tsjerk Wassenaar wrote: > Hi Ankita, > > I had to check the source for this, but -comp writes out the eigenvector as > atom-coordinate components (x,y,z), and the norm of the eigenvector part of > the given atom (total). The numbers are dimensionless. > > Hope it helps, > > Tsjerk > > > On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani > wrote: > > > Hi, > > > > I wanted some help regarding vector components. I.e. when we use the > > g_anaeig command with a flag of -comp, it outputs a file of the > > corresponding eigenvector per atom. So, the x-axis has the atom number > and > > the Y-axis has the total, x, y and z components. I am not sure about what > > do they mean? Also, what are the units of these components? Like the > > numbers on Y-axis, what are the corresponding units? I would be really > > grateful if anyone could kindly help me on this. > > Apologies for reposting but was wondering if anyone has any thoughts on > it? > > > > Best wishes, > > > > -- > > 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. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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] Fwd: Help on the vector component
Hi Ankita, I had to check the source for this, but -comp writes out the eigenvector as atom-coordinate components (x,y,z), and the norm of the eigenvector part of the given atom (total). The numbers are dimensionless. Hope it helps, Tsjerk On Sun, Nov 24, 2013 at 2:38 PM, Ankita Naithani wrote: > Hi, > > I wanted some help regarding vector components. I.e. when we use the > g_anaeig command with a flag of -comp, it outputs a file of the > corresponding eigenvector per atom. So, the x-axis has the atom number and > the Y-axis has the total, x, y and z components. I am not sure about what > do they mean? Also, what are the units of these components? Like the > numbers on Y-axis, what are the corresponding units? I would be really > grateful if anyone could kindly help me on this. > Apologies for reposting but was wondering if anyone has any thoughts on it? > > Best wishes, > > -- > 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. > -- Tsjerk A. Wassenaar, Ph.D. -- 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] Fwd: Help on the vector component
Hi, I wanted some help regarding vector components. I.e. when we use the g_anaeig command with a flag of -comp, it outputs a file of the corresponding eigenvector per atom. So, the x-axis has the atom number and the Y-axis has the total, x, y and z components. I am not sure about what do they mean? Also, what are the units of these components? Like the numbers on Y-axis, what are the corresponding units? I would be really grateful if anyone could kindly help me on this. Apologies for reposting but was wondering if anyone has any thoughts on it? Best wishes, -- 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.