On 1/18/19 11:55 AM, marzieh gharouni wrote:
Hello I did a simulation of protein-protein interaction with Gromacs code. In this simulation, the number of amino acids in each protein is about 230. The simulation production run was 300ns. After analyzing trajectory, I found that RMSD value of protein-protein complex fluctuated near 1.8 nm but the single of each protein has RMSD plots around 0.35 nm. Other plots (rg , rmsf) of the protein-protein complex show my complex system is stable. But I have a problem with the RMSD value (not behavior) of mix proteins. Is it normal? Please see share files Rmsd of protein A-Protein B complex: https://drive.google.com/file/d/16BoOdfUev2Bh7zgUCj4pOBAyPQLS_EJY/view?usp=sharing Rmsd of Protein A: https://drive.google.com/file/d/1QYt2rQQuNK4qqwp9O-k40uglSZaEYjAe/view?usp=sharing Rmsd of protein B: https://drive.google.com/file/d/1DYJ_jIUf-E9I8M38MrBxdh1tAtaIsBod/view?usp=sharing Thanks in advance.
The images mean nothing in the absence of your exact commands and evidence of the groups you selected for analysis (copy and paste all this directly from your terminal).
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
