Dear gromacs users, I’m studying the interaction between protein and several mixture lipids (POPC-MGDG, POPC-DGDG, POPC-SQDG). All simulations ran successfully. Analysing the energy componentes during the simulations i noticed that when i calculated the Coul-SR energy componen Between the protein and each thylakoid membrane i got this:
Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Coul-SR:Protein-DGDG 0 0 0 0 (kJ/mol) And that doesn’t have any sense. Looking into the simulation i noticed how the protein and membranes are interacting, so i don’t know what may be happening (the LJ-SR term showed a more favorable interaction with respect to the thylakoid lipid membrane rather than to the POPC membrane). Is this normal? I’m really worried about these. By the way, i’m using a shift potential to describe coulomb and vdw interactions (since martini force field was parametriced in that way),do you think that maybe this issue is because i’m not using PME to describe this interaction? Best, Carlos -- Carlos Navarro Retamal Bioinformatics Engineering Ph. D (c) Applied Sciences. Center of Bioinformatics and Molecular Simulations. CBSM University of Talca Av. Lircay S/N, Talca, Chile T: (+56) 712201 798 E: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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.
