Hi all, I have simulated a duplex RNA in presence of a CNT in aqueous medium. The gromacs version I used was 4.5.6. The two species were kept 2 nm apart to begin with. I wanted to calculate how many RNA atoms were within 4 angstrom distance from the CNT on a per-frame trajectory basis. I used the following command: g_mindist -f md.xtc -s md.tpr -d 0.4 -n index.ndx -on nc.xvg
The CNT is composed of 1500 atoms while the nucleic acid is 370. The contacts I am getting as a function of time is ~2000. Why is the value so large? I did not specify COM or any particular atom belonging to CNT in my index file and when prompted I selected the entire CNT and RNA for g_mindist analysis. Is the number large because it calculates all the atomic contacts between the two structures and prints it in the .xvg file? For example, at 100 ps if each carbon atom is having at least two RNA contacts then the total contacts will be 3000. Is it being calculated this way or something else is going on? Thank you for your answer in advance Soumadwip Ghosh -- 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.
