Dear Gromacs users, I have a membrane protein simulation performed with gromacs 4.6. I have calculated the minimum distance of protein residues from upper leaflet of the lipid bilayer. I also have the time wise atom pair contacts as an output. The following command i used :
g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx -d 0.7 -o atompair -on numcontact -od mindist.xvg The atom pair out output i got was as follow : .000000e+00 2412 281928 1.000000e+02 1630 266151 2.000000e+02 1630 266151 3.000000e+02 2410 284225 4.000000e+02 2412 284225 5.000000e+02 2412 284225 6.000000e+02 2410 284225 7.000000e+02 2410 284225 8.000000e+02 2410 284225 9.000000e+02 2410 284225 1.000000e+03 2405 284225 1.100000e+03 2411 281928 1.200000e+03 2412 284225 1.300000e+03 2332 285163 1.400000e+03 2411 284225 1.500000e+03 2410 284225 1.600000e+03 1555 264261 1.700000e+03 1555 264261 1.800000e+03 1555 264261 1.900000e+03 1554 266958 2.000000e+03 2389 266958 2.100000e+03 2411 285163 2.200000e+03 2412 285163 2.300000e+03 2412 285163 2.400000e+03 2410 285163 2.500000e+03 2410 285163 2.600000e+03 2412 285163 I now need to find out time wise percentage of protein covering the membrane. I want to know for instance, at time t=0ns, what is the protein coverage % and similarly for the entire trajectory i want to calculate this. Kindly suggest something!! 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.
