Hi all I have DOPC lipid in my system. After preparing index file exactly based on how-to on the g_order page, I used following command to obtain order parameters of acyl chains:
g_order -s md.tpr -f final.xtc -n sn1.ndx -d z -od deuter_sn1.xvg -o order_sn1.xvg I encountered following warnings: WARNING: distance between atoms 779 and 781 > 0.3 nm (1.626940). Index file might be corrupt. WARNING: distance between atoms 995 and 997 > 0.3 nm (0.397073). Index file might be corrupt. WARNING: distance between atoms 1157 and 1159 > 0.3 nm (1.788146). Index file might be corrupt. WARNING: distance between atoms 1265 and 1267 > 0.3 nm (0.828453). Index file might be corrupt. WARNING: distance between atoms 76 and 78 > 0.3 nm (0.747680). Index file might be corrupt. WARNING: distance between atoms 346 and 348 > 0.3 nm (3.898362). Index file might be corrupt. . . . After long time, deuter_sn1.xvg and order_sn1.xvg were obtained. How to remove these warnings? Are these warnings dangerous? Any help will highly appreciated. -- 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.