On 12/13/18 1:05 PM, rose rahmani wrote:
Would you please answer my question? Did you check it?
We can't check your work for you because we don't know what output you
got or why you are suspicious about it. The selections look sensible but
if you ever question if something is working, you need to have a test
case where you know the outcome. If the program doesn't produce the
output you know to be right, likely your approach is wrong. If the
output confirms your suspicions, then you're right.
-Justin
On Wed, 12 Dec 2018, 02:03 Mark Abraham <mark.j.abra...@gmail.com wrote:
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?
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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