On 1/15/14, 9:30 AM, shahab shariati wrote:
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?
The warnings either indicate that the index groups were not constructed properly or that there is some wild behavior going on in the simulation. The printed atom numbers correspond to carbons n-1 and n+1 in the calculation of the order parameters. You can verify that the index groups are good by looking into the coordinate file to make sure they correspond to what you think they do. To verify that the trajectory is sensible, you'll have to visualize it, focusing on the potentially problematic atoms that are printed out.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- 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.
