Hi, I don't really understand how gmx gangke works!!!
I want to calculate angle between amino acid ring and surface during simulation. I mad3 an index for 6 atoms of ring(a_CD1_CD2_CE1_CE2_CZ_CG) and two atoms of surface. Surface is in xy plane and amino acid is in different Z distances. I assumed 6 ring atoms are defining a pkane and two atoms of surface are defining a vector( along Y). And i expected that the Average angle between this plane and vector during simulation is calculated by gmx gangle analysis. gmx gangle -f umbrella36_3.xtc -s umbrella36_3.tpr -n index.ndx -oav angz.xvg -g1 plane -g2 vector -group1 -group2 Available static index groups: Group 0 "System" (4331 atoms) Group 1 "Other" (760 atoms) Group 2 "ZnS" (560 atoms) Group 3 "WAL" (200 atoms) Group 4 "NA" (5 atoms) Group 5 "CL" (5 atoms) Group 6 "Protein" (33 atoms) Group 7 "Protein-H" (17 atoms) Group 8 "C-alpha" (1 atoms) Group 9 "Backbone" (5 atoms) Group 10 "MainChain" (7 atoms) Group 11 "MainChain+Cb" (8 atoms) Group 12 "MainChain+H" (9 atoms) Group 13 "SideChain" (24 atoms) Group 14 "SideChain-H" (10 atoms) Group 15 "Prot-Masses" (33 atoms) Group 16 "non-Protein" (4298 atoms) Group 17 "Water" (3528 atoms) Group 18 "SOL" (3528 atoms) Group 19 "non-Water" (803 atoms) Group 20 "Ion" (10 atoms) Group 21 "ZnS" (560 atoms) Group 22 "WAL" (200 atoms) Group 23 "NA" (5 atoms) Group 24 "CL" (5 atoms) Group 25 "Water_and_ions" (3538 atoms) Group 26 "OW" (1176 atoms) Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms) Group 28 "a_320_302_319_301_318_311" (6 atoms) Group 29 "a_301_302" (2 atoms) Specify any number of selections for option 'group1' (First analysis/vector selection): (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end) > 27 Selection '27' parsed > 27 Selection '27' parsed > Available static index groups: Group 0 "System" (4331 atoms) Group 1 "Other" (760 atoms) Group 2 "ZnS" (560 atoms) Group 3 "WAL" (200 atoms) Group 4 "NA" (5 atoms) Group 5 "CL" (5 atoms) Group 6 "Protein" (33 atoms) Group 7 "Protein-H" (17 atoms) Group 8 "C-alpha" (1 atoms) Group 9 "Backbone" (5 atoms) Group 10 "MainChain" (7 atoms) Group 11 "MainChain+Cb" (8 atoms) Group 12 "MainChain+H" (9 atoms) Group 13 "SideChain" (24 atoms) Group 14 "SideChain-H" (10 atoms) Group 15 "Prot-Masses" (33 atoms) Group 16 "non-Protein" (4298 atoms) Group 17 "Water" (3528 atoms) Group 18 "SOL" (3528 atoms) Group 19 "non-Water" (803 atoms) Group 20 "Ion" (10 atoms) Group 21 "ZnS" (560 atoms) Group 22 "WAL" (200 atoms) Group 23 "NA" (5 atoms) Group 24 "CL" (5 atoms) Group 25 "Water_and_ions" (3538 atoms) Group 26 "OW" (1176 atoms) Group 27 "CE1_CZ_CD1_CG_CE2_CD2" (6 atoms) Group 28 "a_320_302_319_301_318_311" (6 atoms) Group 29 "a_301_302" (2 atoms) Specify any number of selections for option 'group2' (Second analysis/vector selection): (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end) > 29 Selection '29' parsed > 29 Selection '29' parsed > Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision) Reading file umbrella36_3.tpr, VERSION 4.5.4 (single precision) Reading frame 0 time 0.000 Back Off! I just backed up angz.xvg to ./#angz.xvg.1# Last frame 40000 time 4000.Ö00 Analyzed 40001 frames, last ti߸ 4000.000 Am I right? I don't think so. :( Would you please help me? -- 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.