Re: [gmx-users] Re: eigenvectors in readable format
In selecting the eigen vector i just want to make sure about my consideration about the time frames. Should i need to consider the time frame t= 0.0 or i need to start at non zero positive numbers? Thank you. Rama On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar wrote: > Hi Rama, > > You can convert the .trr file to readable .gro/.g96 with trjconv. > Frames with positive times will correspond to eigenvectors; the time > indicates the eigenvector index. Make sure not to use any options like > pbc/fitting :p > > Cheers, > > Tsjerk > > On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G wrote: > > Hi, > > Can anyone help to get the eigen vector in ascii format. I have with me > the > > trajectory file 'eigenvec.trr'. > > > > On using g_covar_d, i got the the ascii format file 'covar.dat' and it > has > > covariance matrix of 3(NxN) number. But i am not interested in that. > > > > I am interested in getting the ascii(readable) format of eigenvector and > > hessian.mtx . > > Your help is highly appreciated. Thank you. > > > > with regards, > > Rama > > > > On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G > wrote: > >> > >> Hi gmx users: > >> I did normal mode analysis and got the hessian.mtx . Using the > command > >> g_nmeig_d on the hessian.mtx > >> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr. > >> > >> I need the complete eigenvector in the readable format. How i can get > it? > >> Thank you. > >> > >> with regards, > >> Rama > >> > >> -- > >> Postdoctoral Research Scholar, > >> Department of Chemistry, > >> University of Nevada, Reno. > > > > > > > > > > > > -- > > 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 > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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: eigenvectors in readable format
Hi Tsjerk, Thank you very much for your help. Cheers! Rama On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar wrote: > Hi Rama, > > You can convert the .trr file to readable .gro/.g96 with trjconv. > Frames with positive times will correspond to eigenvectors; the time > indicates the eigenvector index. Make sure not to use any options like > pbc/fitting :p > > Cheers, > > Tsjerk > > On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G wrote: > > Hi, > > Can anyone help to get the eigen vector in ascii format. I have with me > the > > trajectory file 'eigenvec.trr'. > > > > On using g_covar_d, i got the the ascii format file 'covar.dat' and it > has > > covariance matrix of 3(NxN) number. But i am not interested in that. > > > > I am interested in getting the ascii(readable) format of eigenvector and > > hessian.mtx . > > Your help is highly appreciated. Thank you. > > > > with regards, > > Rama > > > > On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G > wrote: > >> > >> Hi gmx users: > >> I did normal mode analysis and got the hessian.mtx . Using the > command > >> g_nmeig_d on the hessian.mtx > >> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr. > >> > >> I need the complete eigenvector in the readable format. How i can get > it? > >> Thank you. > >> > >> with regards, > >> Rama > >> > >> -- > >> Postdoctoral Research Scholar, > >> Department of Chemistry, > >> University of Nevada, Reno. > > > > > > > > > > > > -- > > 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 > -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- 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: eigenvectors in readable format
Hi Rama, You can convert the .trr file to readable .gro/.g96 with trjconv. Frames with positive times will correspond to eigenvectors; the time indicates the eigenvector index. Make sure not to use any options like pbc/fitting :p Cheers, Tsjerk On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G wrote: > Hi, > Can anyone help to get the eigen vector in ascii format. I have with me the > trajectory file 'eigenvec.trr'. > > On using g_covar_d, i got the the ascii format file 'covar.dat' and it has > covariance matrix of 3(NxN) number. But i am not interested in that. > > I am interested in getting the ascii(readable) format of eigenvector and > hessian.mtx . > Your help is highly appreciated. Thank you. > > with regards, > Rama > > On Fri, Oct 15, 2010 at 2:29 PM, Ramachandran G wrote: >> >> Hi gmx users: >> I did normal mode analysis and got the hessian.mtx . Using the command >> g_nmeig_d on the hessian.mtx >> i got the eigenfreq.xvg, eigenval.xvg, eigenvec.trr. >> >> I need the complete eigenvector in the readable format. How i can get it? >> Thank you. >> >> with regards, >> Rama >> >> -- >> Postdoctoral Research Scholar, >> Department of Chemistry, >> University of Nevada, Reno. > > > > > > -- > gmx-users mailing list gmx-us...@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
