[gmx-users] Gmx gangle (Shi Li)
Li, Shi
sli259 at g.uky.edu
Wed Dec 12 15:59:55 CET 2018
>
>
> > Hi,
> >
> > I would check the documentation of gmx gangle for how it works,
> > particularly for how to define a plane.
>
> Thank you so much Mark. As a GROMACS lover, I like to make a suggestion; I
> think sth it would be REALLY helpful if you provide some proper examples
> for gromacs tools, with results. You have straightforward tutorials and
> useful manual, but some instructions in using tools, are a little ambiguous
> and misleading. This also reduces the number of questions.
>
You only need 3 atoms to define the plane, you may use more than that in
the index, but I think the rest will be ignored, or you may run into some
errors. Simply make an index file (like plane.ndx) with the content:
[ Plane1 ]
atom#1 atom#2 atom3#
[ Vector1 ]
atom#4 atom#5
then include "*-n plane.ndx -g1 plane -g2 vector -group1 Plane1 -group2
Vector1*" in your *gmx gangle* should do the work.
If your vector is sure along the Y axes, you may just use* -g2 y *and
delete the -group2 part. Although I don't think it is good idea to
calculate angle between a plane and a vector, you may lose information of
the rotation along the vector.
Also, I agree with Mark that 4.5.4 is way too old. I will at least use
version 2016 and later. which should fix many bugs.
Have fun!
Shi
>
> > Also, 4.5.4 is prehistoric, please
> > do yourself a favor
>
> I would like, but I remember that I wanted to use cutoff-scheme=group and i
> couldnt come up with errors in gmx. These calculations are for more than
> one year ago (and now I want some more analysis), i was a freshman,
>
> > and use a version with the seven years of improvements
> >
> I was a freshman, dear smiling man -:)
>
> > since then :-)
> >
> I am waiting for you.
>
> Best
>
> >
> > Mark
> >
> > On Tue., 11 Dec. 2018, 10:14 rose rahmani, <rose.rhmn93 at 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.?00
> > > Analyzed 40001 frames, last ti?? 4000.000
> > >
> > > Am I right? I don't think so. :(
> > >
> > > Would you please help me?
> > > --
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