[gmx-users] gmx covar and gmx anaeig

[Özge ENGİN]

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: osensoy at medipol.edu.tr <e-mail%3Aydurmaz at medipol.edu.tr>
Phone:+90 (216) 681-5100 <%280216%29%20681%2051%2000> (5621)
<http://ipont.medipol.edu.tr/>