Dear Gromacs users, Can anyone suggest me a way to find the membrane contact sites i.e. the lipids that are making contact with protein residues with respect to time from a membrane protein simulation? I have calculated the distance and contact of protein residues from upper leaflet atoms of bilayer already with a cutoff between 0.5 nm and 0.7 nm.
I have the lipid numbers in the log file from g_hbond as well as g_dist. Should i be taking all these into account or a cutoff needs to be taken and can this be calculated wrt time? Secondly, has anyone found out the lipid binding strength from membrane protein simulations? Can we call the frequency of a protein residue to make a contact as its lipid binding strength? Here also, is there some way to find the binding strength wrt time? Thanks!! Kind Regards, Antara -- Junior research fellow(project) Systems biology group CSIR-Institute of Genomics & Integrative Biology South Campus New Delhi - 110020 M : +91-9717970040 -- -- 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.