Re: [gmx-users] gmx gangle in a for loop

[Christian Blau]

Hello Alex,


What works for me is setting '$i' within singe quotation marks, e.g.,

'group '$i' and name C10 plus group '$i' and name C20'


Note that this is more of a bash escaping quotes issue and only a GROMACS issue insofar as the selection syntax requires 
the quotes.



Best,

Christian

On 11/6/19 3:32 AM, Alex wrote:

Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.

#!/bin/bash/
for i in {1..1000}
do
 gmx gangle -g1 vector -group1 'group $i and name C10 plus group $i
and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n
ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg
done

Thank you
Alex

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[gmx-users] gmx gangle in a for loop

[Alex]

Dear all,
Could one kindly let me know how $i should come in gmx gangle used in a for
loop to avoid syntax errors?
I tested different flavors like "$i", "${i}", ..., and still the problem is
here.

#!/bin/bash/
for i in {1..1000}
do
gmx gangle -g1 vector -group1 'group $i and name C10 plus group $i
and name C20' -g2 vector -group2 'cog of group 0 plus cog of group $i' -n
ind.ndx -f ind.xtc -s ind.tpr -oav aver$i.xvg -oh hist$i.xvg
done

Thank you
Alex
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Re: [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[atb files]

*Now use gmx gangle command without “-seltype res_com -selrpos 
-res_com” command. Obviously now your index.ndx file have indexes of [1] and 
[2] generated from mapped trajectory.Sent using Zoho Mail On Wed, 03 Jul 
2019 13:59:39 +0530  Vikas Dubey wrote Dear all,  
I have been trying to use gmx gangle for the calculation of the following angle 
: I have a group of 3 residues and another group of 4 residues. I want to 
define a vector which goes through the center of mass of these two groups and I 
am interested in calculating the angle  of the vector w.r.t to the Z-axis, 
which seems doable from the gmx gangle. based on the documentation, I write the 
following :  *gmx angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z 
-group1  -seltype res_com 
-selrpos -res_com -oav -all   *  but I don't think this is correct because I am 
calculating the center of mass of whole group. Is there a way to calculate this 
angle?  Thanks, --  Gromacs Users mailing list  * Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!  * 
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Re: [gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[atb files]

Hi Vikas,One way is transform your atomic trajectory to center of 
mass position trajectory. You can do it by first removing periodic breakages by 
running gmx trjconv -s gromos.tpr -f gromos.xtc -pbc whole -o whole.xtc Then 
run below command to get transform the atomic to center of mass position 
trajectory gmx traj -f whole.xtc -s gromos.tpr -oxt mapped.xtc -n mapping.ndx 
-com -ng 2Your mapping.ndx file should look like this (for example)[ 1 ] 1 2 3 
[ 2 ] 5 6 7In your case, group1 is define by [1] where you will define index 
numbers of 3 residues, in place of 1 2 3 and of 4 residues for group [2].Now 
use gmx gangle command with  “-seltype res_com -selrpos -res_com” command. 
Obviously now your index.ndx file have indexes of [1] and [2] generated from 
mapped trajectory.-Yogesh Sent using Zoho Mail On Wed, 03 Jul 2019 13:59:39 
+0530  Vikas Dubey wrote Dear all,  I have been 
trying to use gmx gangle for the calculation of the following angle : I have a 
group of 3 residues and another group of 4 residues. I want to define a vector 
which goes through the center of mass of these two groups and I am interested 
in calculating the angle  of the vector w.r.t to the Z-axis, which seems doable 
from the gmx gangle. based on the documentation, I write the following :  *gmx 
angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z -group1 
 -seltype res_com -selrpos 
-res_com -oav -all   *  but I don't think this is correct because I am 
calculating the center of mass of whole group. Is there a way to calculate this 
angle?  Thanks, --  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 
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[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[Vikas Dubey]

Dear all,

I have been trying to use gmx gangle for the calculation of the following
angle :
I have a group of 3 residues and another group of 4 residues. I want to
define a vector which goes through the center of mass of these two groups
and I am interested in calculating the angle  of the vector w.r.t to the
Z-axis, which seems doable from the gmx gangle.
based on the documentation, I write the following :

*gmx angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z -group1
 -seltype res_com
-selrpos -res_com -oav -all   *

but I don't think this is correct because I am calculating the center of
mass of whole group. Is there a way to calculate this angle?

Thanks,
-- 
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[gmx-users] gmx gangle : How to calculate the angle between a vector and Z axis?

[Vikas Dubey]

Dear all,

I have been trying to use gmx gangle for the calculation of the following
angle :
I have a group of 3 residues and another group of 4 residues. I want to
define a vector which goes through the center of mass of these two groups
and I am interested in calculating the angle  of the vector w.r.t to the
Z-axis, which seems doable from the gmx gangle.
based on the documentation, I write the following :

*gmx angle -f traj.xtc -s topol.tpr -n index.ndx -g1 -vector -g2 z -group1
 -seltype res_com
-selrpos -res_com -oav -all   *

but I don't think this is correct because I am calculating the center of
mass of whole group. Is there a way to calculate this angle?

Thanks,
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

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Re: [gmx-users] Gmx gangle

[Justin Lemkul]

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 
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,  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,  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,  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 time0.000
Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
Last frame  4 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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send a mail to 

Re: [gmx-users] Gmx gangle

[rose rahmani]

Would you please answer my question? Did you check it?

On Wed, 12 Dec 2018, 02:03 Mark Abraham  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,  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,  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,  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 time0.000
> > Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
> > Last frame  4 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!
> >
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> >
> > * 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.
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> * Please search the archive at
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-- 
Gromacs 

Re: [gmx-users] Gmx gangle (Shi Li)

[Li, Shi]

>
>
> > 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, 
> 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,  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)
> > >  

Re: [gmx-users] Gmx gangle

[rose rahmani]

On Wed, 12 Dec 2018, 02:03 Mark Abraham  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.

> 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,  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,  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,  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 time0.000
> > Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
> > Last frame  4 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 

Re: [gmx-users] Gmx gangle

[Mark Abraham]

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,  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,  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,  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 time0.000
> Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
> Last frame  4 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
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[gmx-users] Gmx gangle

[rose rahmani]

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,  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,  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 time0.000
Back Off! I just backed up angz.xvg to ./#angz.xvg.1#
Last frame  4 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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Re: [gmx-users] Gmx gangle

[rose rahmani]

Is sth wrong or unclear in my question?


On Sun, 9 Sep 2018, 15:01 rose rahmani,  wrote:

> Sorry,
> BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .
>
> How should i define the surface plane?
>
> On Sun, 9 Sep 2018, 14:45 rose rahmani,  wrote:
>
>> Hi,
>>
>> I want to calculate angle between water molecules and ZnS surface(slab).
>> I mean the angular distribution function(ADF) of ALPHA and BETA. I define
>> to angles; Alpha= angle between OH bond of water and  surface(plane)
>> Beta= angle between HOH plane and surface(plane).
>>
>> I used gmax gangle for Alpha:
>> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
>> Then i selected water(SOL) group
>>
>> For Beta:
>> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
>> And again i selected water group.
>>
>> But results are little odd and histograms are two plot which are
>> symmetric plots.
>>
>> I think sth is wrong. Should i make an index file for OH bond in the case
>> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
>> calculated the angle between COM of water vector and surface not the OH
>> bond of water. As you know water has 2 OH bond. So... what should i do?
>>
>> How about BETA? does it really calculate what i want?
>>
>> Should i make an special index file?
>>
>> If i want to calculate this property (ADF) in for example 1 nm from
>> surface, what should i do?
>>
>> To be more clear, I refer you to fig.1 and fig.8
>> roja:
>>
>> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures
>>
>> Would you please help me how can i reach these goals?
>>
>> Best regards
>>
>> Rose
>>
>>
>>
>>
>>
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Re: [gmx-users] Gmx gangle

[rose rahmani]

Sorry,
BTW, the slab is in xy plane. But i get an error when i use -g2 y or x .

How should i define the surface plane?

On Sun, 9 Sep 2018, 14:45 rose rahmani,  wrote:

> Hi,
>
> I want to calculate angle between water molecules and ZnS surface(slab). I
> mean the angular distribution function(ADF) of ALPHA and BETA. I define to
> angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
> angle between HOH plane and surface(plane).
>
> I used gmax gangle for Alpha:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
> Then i selected water(SOL) group
>
> For Beta:
> Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
> And again i selected water group.
>
> But results are little odd and histograms are two plot which are symmetric
> plots.
>
> I think sth is wrong. Should i make an index file for OH bond in the case
> of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
> calculated the angle between COM of water vector and surface not the OH
> bond of water. As you know water has 2 OH bond. So... what should i do?
>
> How about BETA? does it really calculate what i want?
>
> Should i make an special index file?
>
> If i want to calculate this property (ADF) in for example 1 nm from
> surface, what should i do?
>
> To be more clear, I refer you to fig.1 and fig.8
> roja:
>
> https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures
>
> Would you please help me how can i reach these goals?
>
> Best regards
>
> Rose
>
>
>
>
>
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[gmx-users] Gmx gangle

[rose rahmani]

Hi,

I want to calculate angle between water molecules and ZnS surface(slab). I
mean the angular distribution function(ADF) of ALPHA and BETA. I define to
angles; Alpha= angle between OH bond of water and  surface(plane)Beta=
angle between HOH plane and surface(plane).

I used gmax gangle for Alpha:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 vector -g2 z -oh
Then i selected water(SOL) group

For Beta:
Gmx gangle -f traj.xtc -s topol.tpr -n index.ndx -g1 plane -g2 z -oh
And again i selected water group.

But results are little odd and histograms are two plot which are symmetric
plots.

I think sth is wrong. Should i make an index file for OH bond in the case
of ALPHA? If yes how bonds defined in gmx make_ndx? because i think it
calculated the angle between COM of water vector and surface not the OH
bond of water. As you know water has 2 OH bond. So... what should i do?

How about BETA? does it really calculate what i want?

Should i make an special index file?

If i want to calculate this property (ADF) in for example 1 nm from
surface, what should i do?

To be more clear, I refer you to fig.1 and fig.8
roja:
https://www.researchgate.net/publication/257760740_Structural_properties_of_water_around_uncharged_and_charged_carbon_nanotubes/figures

Would you please help me how can i reach these goals?

Best regards

Rose
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Re: [gmx-users] gmx gangle

[Antonio Baptista]

Hi João,

I used gangle to compute several angle distributions relative to the 
z-axis membrane normal, but that was almost a year ago, so I don't recall 
the details. But I can tell you that, after many failed attempts, I gave 
up from using fancy stuff in the -group1 and -group2 options. Instead, I 
ended up writing a small bash script to process one atom pair at a time 
(just one group in the .ndx file per gangle run) and to collect everything 
at the end.


I understand that your problem is a bit different (your second vector is 
not an axis, but defined by a second atom pair), but maybe a similar 
"minimalist" approach could get the job done. Or not... Good luck!


Best,
Antonio

On Wed, 15 Feb 2017, João Henriques wrote:


Hello everyone,

It seems that my inquiries about gmx gangle and selections are either too
funky or too basic to justify getting a single answer from the community.
Still, I will try once more with an even simpler scenario, which will
hopefully attract an answer (even if it's just someone telling me to stop
reposting, despite the fact that it is not 100% a repost).

I have a trajectory where the water molecules are ordered by proximity to
the protein. I also have an index file with the N closest waters that I am
interested in analyzing. Now, my plan is to simply compute the O-H angle
distribution within the group composed by these N water molecules. For that
I type something along these lines:

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
"hydration_shell" and name OW HW1" -g2 vector -group2 "group
"hydration_shell" and name OW HW1" -oav -oall -oh

To my surprise, this command returns something completely different from
what I expected. Instead of the angular distribution function of all pairs
of O-H vectors from different water molecules, it outputs zero. Obviously,
this means that the command is computing the angle between the O-H vector
of each water molecule and itself. How can I modify my selection to produce
the desired result?

Thank you in advance,
Best regards,
João
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[gmx-users] gmx gangle

[João Henriques]

Hello everyone,

It seems that my inquiries about gmx gangle and selections are either too
funky or too basic to justify getting a single answer from the community.
Still, I will try once more with an even simpler scenario, which will
hopefully attract an answer (even if it's just someone telling me to stop
reposting, despite the fact that it is not 100% a repost).

I have a trajectory where the water molecules are ordered by proximity to
the protein. I also have an index file with the N closest waters that I am
interested in analyzing. Now, my plan is to simply compute the O-H angle
distribution within the group composed by these N water molecules. For that
I type something along these lines:

gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
"hydration_shell" and name OW HW1" -g2 vector -group2 "group
"hydration_shell" and name OW HW1" -oav -oall -oh

To my surprise, this command returns something completely different from
what I expected. Instead of the angular distribution function of all pairs
of O-H vectors from different water molecules, it outputs zero. Obviously,
this means that the command is computing the angle between the O-H vector
of each water molecule and itself. How can I modify my selection to produce
the desired result?

Thank you in advance,
Best regards,
João
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[gmx-users] gmx gangle selections help

[Eric Smoll]

Hello gromacs users,

I want to map the angle between a specific bond vector (defined by the
atoms A and B) and the z axis using gmx gangle. I am only interested in
bond vectors that have a center-of-mass z-coordinate greater than C. Is
there a way to make this selection using the 'gmx select'-type statements?
I suspect that the selection below will not produce an appropriately paired
set of bond atoms. Am I correct?

-g1 vector
-g2  z
-group1 ''resname LIG and name A B and part_res_com z > C"

Best,
Eric
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[gmx-users] gmx gangle failure after assigning zero-charges

[Thomas Niklas]

Hi there,
I have been using GROMACS version 5.0.6 to perform some simple MD 
Simulations that involve a polystyrene strand and a single further 
molecule (e.g. toluene). I wanted to observe some angles between both 
molecules so after I produced a trajectory, I applied "gmx gangle" and 
everything worked just perfectly. I subsequently employed a topology in 
which I did not change anything except that I assigned zero-charges 
(instead of standard OPLS-AA values) to all atoms and produced another 
trajectory.

In this case analysis with "gmx gangle" immediately aborts with:

.../gromacs-5.0.6/src/gromacs/gmxlib/pbc.c, line: 81

Fatal error:
Unknown ePBC=38063816 in ePBC2npbcdim

I am following basic procedures with these simulations, since I have not 
much experience in MD. However, I think this is a bit odd and probably 
not my fault? I further guess that, since I have trajectories, I can 
also utilize something like vmd or travis to also get the angles I am 
interested in?

Thank you and best regards,
Thomas Niklas
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Re: [gmx-users] gmx gangle in the development version of gromacs

[LIANG Xujun]

Dear Eric.

I am now also calculating the angle between normal vector of plane 1 and com 
vector of plane 1 and plane 2. I also use the following command you used in the 
mail (with small modifications).

gmx gangle -f file.trr -s file.tpr -n  file.ndx -g1 plane -group1 'z 0 to 1
and group a_plane' -g2 z -oh file.xvg -binw 1.0

However, I wonder if the –g1 plane –group1 group a plane could indicate that we 
want the normal of the plane, when –g2 is set as vector. Since I used the 
following command:

gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 plane -group1 plane 1 (I tried to use 
this command to select the normal vector of plane 1, but it doesn't work!!) -g2 
vector -group2 com of group 1 plus com of group 2 (use this to define the COM 
vector) -oav *.xvg

But unfortunately, the results I obtained were the angle between plane 1 and 
COM vector, not normal vector of plane 1 with COM vector. Thus, couly you 
please help me to define the plane normal vector in gromacs 5.0.4??

Thanks in advance!

Best, 
Xujun

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Re: [gmx-users] gmx gangle in the development version of gromacs

[Teemu Murtola]

On Thu, Mar 6, 2014 at 1:48 AM, Eric Smoll ericsm...@gmail.com wrote:

  As you have noted, whole_res_cog computes the center-of-geometry of the
  whole residue that contains an individual atom. So if each of your rings
 is
  within a single residue, this makes then selected as a unit, based on the
  center of the whole residue. If you only want to select based on the
 center
  of the ring, you can use part_res_cog. The difference is explained in
 'gmx
  help selections positions' (accessible also when writing help in the
  interactive selection prompt).

 I will try part_res_cog but I suspect it is not what I want. 'gmx help
 selections positions'
 states:
 part_ prefix calculates the centers for the selected atoms, but uses
 always the same atoms
 for the same residue/molecule. The used atoms are determined from the the
 largest group allowed by the selection.
 This first sentence sounds like it may preform the selection I desire but
 the second
 sentence is worrisome.  I have a molecule with a ring. My index file
 selects three atoms from this molecule to monitor - three atoms are needed
 for an normal
 vector calculation. If a cog is in the selection region but only one of the
 three atoms that
 define a given cog are in the selection region, will 'part_res_cog' result
 in the selection of all three atoms?


Yes, it will. If you have a selection like
  name A B C and z  0
and your residue has atoms A B C D E, then

   - -selrtype whole_res_cog will select either all or none of A-C, based
   on the CoG of A-E.
   - -selrtype part_res_cog will select either all or none of A-C, based on
   the CoG of A-C.
   - -selrtype dyn_res_cog will in this case do the same as part_res_cog.
   It requires quite a complex selection to make a difference between the two
   (for example, name A B C and atom z  0 and dyn_res_cog x  0, in which
   case the second x  0 condition only compares based on the CoG of the
   atoms that satisfy z  0). This is probably confusing and not usually
   necessary; it mostly makes sense as an output option from the selections
   only: dyn_res_cog of name A B C and z  0 computes the output position
   from those atoms that actually satisfy the z  0 condition.

If the residue index controls which atoms are grouped in a given 'residue',
 what
 controls the molecule specification?  What is it in the .gro file that
 defines an
 atom as belonging to a specific molecule?


There is nothing in a .gro file that specifies a molecule. This option only
works with a full .tpr file, in which case the molecule definitions from
the simulation topology are used.

This sounds like a very straightforward solution! I read up on the format
 of the
 .gro file.  It makes sense that I should be free to manipulate the residue
 numbers
 but are they any restrictions? For example. do the residue numbers need to
 be grouped and
 consecutive? I ask because a separate software (VMD) will not support
 residue number reassignment
 of various nonconsecutive atoms without disrupting the residue selection
 algorithm.


In Gromacs, a group of consecutive atoms with the same residue number is
treated as a single residue. If the same residue number repeats elsewhere,
then it is a different residue. There is no requirement on the numbers of
different residues being consecutive. So the atoms in a residue need to be
grouped together, but there are no other restrictions. Depending on what
you want to do with the numbers, it can be confusing, though, if the same
number repeats.

Teemu
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[gmx-users] gmx gangle in the development version of gromacs

[Eric Smoll]

Hello gromacs users,

I want to analyze a liquid interface by producing a series of histograms
that profile different slices of my simulation along the cartesian z axis.
In each histogram, I want to bin the angles between the z-axis and the
normal vector defined by a plane of three atoms in a flat molecular ring. I
have many of these rings in my simulation.

I downloaded the development version of gromacs and read the documentation
associated with g_select and gmx gangle.

As I understand it, my index file should select the atoms that define each
normal vector. To properly profile a slice, the selection should be
dynamic. Atoms *defining the plane* that drift into a slice during a
simulation must be selected. Atoms *defining the plane* that drift out of a
slice must be deselected. Also, it would be nice to make this spatial
dynamic selection based on the center of geometry of the *atoms that define
the plane* or some other sensible molecular substructure.

My index file looks something like this...

[ a_plane ]
1 2 3
10 11 12
...

...where each row lists that ring atoms that define the plane in exactly
the same way.

Assuming I define a given slice to be between 0 and 1 on the z axis, I
believe the command that will produce what I want is:

gmx gangle -f file.trr -s file.tpr -n  file.ndx -g1 plane -group1 'z 0 to 1
and group a_plane' -g2 z -oh file.xvg -binw 1.0

A few questions/comments:

1.) I am unsure how I should set the '-selrpos' option. The gangle program
requires all three atoms to compute the angle so I suspect that the prefix
'whole_' is necessary. What is the difference between the res_ and mol_
infix?  I was hoping the index file would restrict the computation of the
reference position so that 'whole_res_cog' would work but it seems to
compute the cog for the whole residue, not that atoms that define the
plane.  For clarity, if the cog of the three atoms that define the plane
lie within the slice, I want all three atoms that define the plane to be
selected.

2.) Is it possible to use a custom set of atoms for computation of the cog
that differs from the atoms I want selected if this cog is within the
slice?  For example, consider benzene. The program gangle requires three
benzene atoms to define a plane but the cog of these atoms is not the cog
of the ring.  I suspect this is not possible with the gromacs tools.

2.) It seems the flag '-oall' outputs the angles for all the normal vectors
defined by the atoms in my index file.  Is this want most users will want
from this tool?  If I have selection like 'z 0 to 1 and group a_plane', it
makes more sense for '-oall' to print all the selected angles, correct?

Best,
Eric
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