[gmx-users] gmx covar and gmx anaeig

[David van der Spoel]

Den 2019-01-31 kl. 12:28, skrev 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.
These are very crude methods that may or may not tell you anything about 
the systems under study. They are also strongly dependent on sampling. 
So your results means that A) you did long enough sampling as proved 
througn an independent method and there is little difference between the 
systems or B) your results are inconclusive.

> 
> 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/>
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se