Hi, I would check the documentation of gmx gangle for how it works, particularly for how to define a plane. Also, 4.5.4 is prehistoric, please do yourself a favor and use a version with the seven years of improvements since then :-)
Mark On Tue., 11 Dec. 2018, 10:14 rose rahmani, <rose.rhm...@gmail.com> wrote: > 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. -- 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.
