[gmx-users] gmx distance
Hello Dear All I did a simulation of protein-protein interaction. I want to obtain a distance residue between the two proteins. In the Gromacs tutorial has been said to calculate of distance for protein-ligand whereas I want to calculate of distance for protein-protein. The command of protein-ligand in the Gromacs tutorial: gmx distance -s md_0_10.tpr -f md_0_10_center.xtc -select 'resname "JZ4" and name OAB plus resid 102 and name OE1' -oall can I use resid instead of resname for protein because I have two proteins? I would be grateful if you could say command of distance for residues between two proteins. Thank's a lot. -- 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.
[gmx-users] Periodic Boundary Conditions
Hello I want to do noPeriodic Boundary Conditions for my system. Gromacs tutorial has said that it can not be used the center and nojump in one command simultaneously. I would be grateful if you could explain the reasons for it? please see this tutorial http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Thanks a lot. -- 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.
[gmx-users] RMSD plots protein-protein complex
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. -- 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.
[gmx-users] (no subject)
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