[gmx-users] RE: quasi-harmonic entropy calculation
Hi, IIRC I tested g_anaeig when David wrote it and the results were the same as calc_entropies.pl, so it sounds strange. Are you sure you use the same input in both cases? Did you use the eigenvectors that correspond to the same eigenvalues? Also, how may eigenvalues are close to zero? Ran Message: 4 Date: Thu, 22 Mar 2012 10:27:36 -0400 From: wmira...@estudiantes.fbio.uh.cu Subject: [gmx-users] Re: quasi-harmonic entropy calculation To: gmx-users@gromacs.org Message-ID: <5e667c140e0c268c9e87681be3535b89.squir...@est.fbio.uh.cu> Content-Type: text/plain;charset=iso-8859-1 My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks -- 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: quasi-harmonic entropy calculation
Op 22 mar 2012 om 15:27 heeft wmira...@estudiantes.fbio.uh.cu het volgende geschreven: > My name is Williams. I am a Biochemistry student. I have done QH entropy > calculation using g_anaeig, but I found an old perl script at GROMACS web > site to do the same. The problem is that when I calculate entropy for the > loops of my protein the results are the same using g_anaeig or the old > perl script, but when I compare the entropy calculated through both > methods for my entire protein the results diverges in one order of > magnitud and I give to the script the same eigenvalues obtained by g_covar > (g_anaeig uses the eigenvectors). Please, help me. > Thanks Is there readon to assume g_anaeig is incorrect? There is numerical problem with this calculation due to the large range of numbers and therefore the g_anaeig program uses ligarithms. Please compare the source code in case of doubt. > > -- > 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
[gmx-users] Re: quasi-harmonic entropy calculation
My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks -- 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
