Hi All, I am working on 3 systems in parallel: 1) protein only, 2) protein+ligand1 and 3) protein+ligand2 using the same protein. Here, I want to get rmsf profiles of the systems along the first and second eigenvectors which can be get by gmx anaeig -rmsf option. I want to use the eigenvectors pertaining to protein only system and project the rest on to these eigenvectors to make a reasonable comparison. To do so, I used the following command lines:
A) gmx covar on Protein_only trajectory B) gmx anaeig protein+ligand1 trajectory + eigenvectors of protein only what I get is similar rmsf profiles from A and B. Sure i am missing something but could not find. Thanks, Best, Ozge *Özge Şensoy, Ph.D.* Assistant Professor Department of Computer Engineering School of Engineering and Natural Sciences Istanbul Medipol University Kavacik Mah., Ekinciler Cad. No:19 34810 Beykoz, Istanbul e-mail: osen...@medipol.edu.tr <e-mail%3aydur...@medipol.edu.tr> Phone:+90 (216) 681-5100 <%280216%29%20681%2051%2000> (5621) <http://ipont.medipol.edu.tr/> -- 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.
