Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey 
Hi Justin,

Yes I understand what you are saying.

Thank you

amit

On Wed, Dec 2, 2009 at 12:50 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>
>>
>> On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>That is true. But what does the manual refer to when it says
>>the first graph is the average, the rest are the individual angles
>>
>>what and where are the rest? I am only curious because there
>>might be a hidden feature that could be useful for me.
>>
>>
>>Read all of the help information; the command in the .xvg file below
>>shows that you're not yet using the right output options.  Hint:
>>look at the sentence in g_angle -h before the one quoted above, as
>>well as the -ov flag...
>>
>>
>> -ov flag gives the average value of angle of the group with time. This is
>> not very useful for me right now.
>>
>
> By using -ov -all, the first column is the average of all groups analyzed,
> and probably is not useful for your purpose, but the subsequent columns are
> the value of the chosen angles at each time frame.  From these data, you
> could pretty easily write a script that calculates the distributions by
> binning.
>
> -Justin
>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Justin A. Lemkul 



Amit Choubey wrote:



On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul > wrote:




Amit Choubey wrote:

Hi Mark,

That is true. But what does the manual refer to when it says
the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there
might be a hidden feature that could be useful for me.


Read all of the help information; the command in the .xvg file below
shows that you're not yet using the right output options.  Hint:
look at the sentence in g_angle -h before the one quoted above, as
well as the -ov flag...


-ov flag gives the average value of angle of the group with time. This 
is not very useful for me right now.


By using -ov -all, the first column is the average of all groups analyzed, and 
probably is not useful for your purpose, but the subsequent columns are the 
value of the chosen angles at each time frame.  From these data, you could 
pretty easily write a script that calculates the distributions by binning.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey 
On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> That is true. But what does the manual refer to when it says
>> the first graph is the average, the rest are the individual angles
>>
>> what and where are the rest? I am only curious because there might be a
>> hidden feature that could be useful for me.
>>
>>
> Read all of the help information; the command in the .xvg file below shows
> that you're not yet using the right output options.  Hint: look at the
> sentence in g_angle -h before the one quoted above, as well as the -ov
> flag...
>

-ov flag gives the average value of angle of the group with time. This is
not very useful for me right now.

I am interested in the distribution of dihedrals with angle.

I was just curious about the -all features...



>
> -Justin
>
>  Amit
>>
>>
>> On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>Ok here is the command line i used :-
>>
>>g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>804 -all
>>output is
>># This file was created Tue Dec  1 20:20:41 2009
>># by the following command:
>># g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>804 -all
>>#
>># g_angle is part of G R O M A C S:
>>#
>># Go Rough, Oppose Many Angry Chinese Serial killers
>>#
>>@title "Dihedral Distribution: C34_C36_C37_C38"
>>
>>
>>This title makes it look like there is only one angle in your index
>>file.
>>
>>Mark
>>
>>@xaxis  label "Degrees"
>>@yaxis  label ""
>>@TYPE xy
>>@subtitle "average angle: 9.87432\So\N"
>>@with g0
>>@world xmin -180
>>@world xmax  180
>>@world ymin 0
>>@world ymax 0.0451172
>>@xaxis  tick major 60
>>@xaxis  tick minor 30
>>@yaxis  tick major 0.005
>>@yaxis  tick minor 0.0025
>> -1800.015625
>> -1790.011719
>> -1780.015625
>> -1770.00
>> -1760.035156
>> -1750.031250
>> -1740.019531
>> -1730.019531
>> -1720.023438
>> -1710.015625
>> -1700.015625
>>
>>I did not include the distribution for rest of the angles.
>> The second column is the fractional distribution of dihedrals
>>with the corresponding angle in the 1st column.
>>
>>The distribution is averaged over time t = 800ps and 802 ps
>>snapshots. I checked this part.
>>
>>Amit
>>
>>
>>
>>
>>On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> wrote:
>>
>>   Amit Choubey wrote:
>>
>>   Hi Mark,
>>
>>   It does seem that the -all option averages the
>> distributions.
>>   The thing is i was confused with "the first graph is the
>>   average, the rest are the individual angles." because when i
>>   tried it previously i only found 2 columns which were
>>angle and
>>   distribution.
>>
>>   But now i checked again explicitly by doing few more g_angle
>>   commands and it seems that -all does do what i wanted to
>>do. I
>>   still dont know what the "rest are the individual angles"
>>means.
>>
>>
>>   I haven't ever used it, but would have expected the output to be
>>   along the lines of
>>
>>   Time "Average over all angles" Angle-1 Angle-2 ...
>>   1  234   23  345
>>   2  123   234 232
>>   2  223   ...
>>   3  323
>>
>>   What output do you get and what seems wrong to you?
>>
>>   Mark
>>
>>   On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
>>   mailto:mark.abra...@anu.edu.au>
>>>
>>   >
>>   >>
>>  Amit Choubey wrote:
>>
>>  Hi everyone,
>>
>>  I am trying to analyze dihedrals of molecules after a
>>  simulation. I am able to calculate dihedral
>>distribution
>>   at ant
>>  particular time using g
>>  -angle and proper group using
>>
>>  g_angle -f after_md.trr -b 800 -type dihedral -n
>>

Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Justin A. Lemkul 



Amit Choubey wrote:

Hi Mark,

That is true. But what does the manual refer to when it says 


the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there might be a 
hidden feature that could be useful for me.




Read all of the help information; the command in the .xvg file below shows that 
you're not yet using the right output options.  Hint: look at the sentence in 
g_angle -h before the one quoted above, as well as the -ov flag...


-Justin


Amit

On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham > wrote:


Amit Choubey wrote:

Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
804 -all
output is
# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title "Dihedral Distribution: C34_C36_C37_C38"


This title makes it look like there is only one angle in your index
file.

Mark

@xaxis  label "Degrees"
@yaxis  label ""
@TYPE xy
@subtitle "average angle: 9.87432\So\N"
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
 -1800.015625
 -1790.011719
 -1780.015625
 -1770.00
 -1760.035156
 -1750.031250
 -1740.019531
 -1730.019531
 -1720.023438
 -1710.015625
 -1700.015625

I did not include the distribution for rest of the angles.
 The second column is the fractional distribution of dihedrals
with the corresponding angle in the 1st column.

The distribution is averaged over time t = 800ps and 802 ps
snapshots. I checked this part.

Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   Amit Choubey wrote:

   Hi Mark,

   It does seem that the -all option averages the distributions.
   The thing is i was confused with "the first graph is the
   average, the rest are the individual angles." because when i
   tried it previously i only found 2 columns which were
angle and
   distribution.

   But now i checked again explicitly by doing few more g_angle
   commands and it seems that -all does do what i wanted to
do. I
   still dont know what the "rest are the individual angles"
means.


   I haven't ever used it, but would have expected the output to be
   along the lines of

   Time "Average over all angles" Angle-1 Angle-2 ...
   1  234   23  345
   2  123   234 232
   2  223   ...
   3  323

   What output do you get and what seems wrong to you?

   Mark

   On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>

Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Amit Choubey 
Hi Mark,

That is true. But what does the manual refer to when it says

the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there might be a
hidden feature that could be useful for me.

Amit

On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> Ok here is the command line i used :-
>>
>> g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
>> output is
>> # This file was created Tue Dec  1 20:20:41 2009
>> # by the following command:
>> # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
>> #
>> # g_angle is part of G R O M A C S:
>> #
>> # Go Rough, Oppose Many Angry Chinese Serial killers
>> #
>> @title "Dihedral Distribution: C34_C36_C37_C38"
>>
>
> This title makes it look like there is only one angle in your index file.
>
> Mark
>
>  @xaxis  label "Degrees"
>> @yaxis  label ""
>> @TYPE xy
>> @subtitle "average angle: 9.87432\So\N"
>> @with g0
>> @world xmin -180
>> @world xmax  180
>> @world ymin 0
>> @world ymax 0.0451172
>> @xaxis  tick major 60
>> @xaxis  tick minor 30
>> @yaxis  tick major 0.005
>> @yaxis  tick minor 0.0025
>>  -1800.015625
>>  -1790.011719
>>  -1780.015625
>>  -1770.00
>>  -1760.035156
>>  -1750.031250
>>  -1740.019531
>>  -1730.019531
>>  -1720.023438
>>  -1710.015625
>>  -1700.015625
>>
>> I did not include the distribution for rest of the angles.
>>  The second column is the fractional distribution of dihedrals with the
>> corresponding angle in the 1st column.
>>
>> The distribution is averaged over time t = 800ps and 802 ps snapshots. I
>> checked this part.
>>
>> Amit
>>
>>
>>
>>
>> On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>It does seem that the -all option averages the distributions.
>>The thing is i was confused with "the first graph is the
>>average, the rest are the individual angles." because when i
>>tried it previously i only found 2 columns which were angle and
>>distribution.
>>
>>But now i checked again explicitly by doing few more g_angle
>>commands and it seems that -all does do what i wanted to do. I
>>still dont know what the "rest are the individual angles" means.
>>
>>
>>I haven't ever used it, but would have expected the output to be
>>along the lines of
>>
>>Time "Average over all angles" Angle-1 Angle-2 ...
>>1  234   23  345
>>2  123   234 232
>>2  223   ...
>>3  323
>>
>>What output do you get and what seems wrong to you?
>>
>>Mark
>>
>>On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> wrote:
>>
>>   Amit Choubey wrote:
>>
>>   Hi everyone,
>>
>>   I am trying to analyze dihedrals of molecules after a
>>   simulation. I am able to calculate dihedral distribution
>>at ant
>>   particular time using g
>>   -angle and proper group using
>>
>>   g_angle -f after_md.trr -b 800 -type dihedral -n
>>chain1.ndx -od
>>   dihed12
>>
>>   This gives me the distribution at t=800 ps . What i
>>really want
>>   is to see the dihedral distribution at all time steps
>>(after 800
>>   ps) in one go, and may be do some averaging later. Is there
>> a
>>   straight forward way to do this. I can imagine that i could
>>   write a script file that could do this but then i dont
>>want to
>>   deal with a lot of files, i rather want everything to be
>>saved
>>   in a single file with multiple columns. Could someone
>>suggest a
>>   trick for this?
>>
>>
>>   The first paragraph of g_angle -h suggests there's an option
>>where
>>   "the first graph is the average, the rest are the individual
>>   angles." Does this work?
>>
>>
>>   Mark
>>   --gmx-users mailing listgmx-users@gromacs.org
>>
>>   >
>>
>>
>>   http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at http://www.gromacs.org/searchbefore
>>   posting!
>>   Please don't post (un)subscribe requests to the list. Use the
>> www
>>   interface or send it to gmx-users-requ...@gromacs.org
>>
>>

Re: [gmx-users] doing averages using g_angle

2009-12-02 Thread Mark Abraham 

Amit Choubey wrote:

Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all 

output is 


# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title "Dihedral Distribution: C34_C36_C37_C38"


This title makes it look like there is only one angle in your index file.

Mark


@xaxis  label "Degrees"
@yaxis  label ""
@TYPE xy
@subtitle "average angle: 9.87432\So\N"
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
  -1800.015625
  -1790.011719
  -1780.015625
  -1770.00
  -1760.035156
  -1750.031250
  -1740.019531
  -1730.019531
  -1720.023438
  -1710.015625
  -1700.015625

I did not include the distribution for rest of the angles.
 
The second column is the fractional distribution of dihedrals with the 
corresponding angle in the 1st column.


The distribution is averaged over time t = 800ps and 802 ps snapshots. I 
checked this part.


Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham > wrote:


Amit Choubey wrote:

Hi Mark,

It does seem that the -all option averages the distributions.
The thing is i was confused with "the first graph is the
average, the rest are the individual angles." because when i
tried it previously i only found 2 columns which were angle and
distribution.

But now i checked again explicitly by doing few more g_angle
commands and it seems that -all does do what i wanted to do. I
still dont know what the "rest are the individual angles" means.


I haven't ever used it, but would have expected the output to be
along the lines of

Time "Average over all angles" Angle-1 Angle-2 ...
1  234   23  345
2  123   234 232
2  223   ...
3  323

What output do you get and what seems wrong to you?

Mark

On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> wrote:

   Amit Choubey wrote:

   Hi everyone,

   I am trying to analyze dihedrals of molecules after a
   simulation. I am able to calculate dihedral distribution
at ant
   particular time using g
   -angle and proper group using

   g_angle -f after_md.trr -b 800 -type dihedral -n
chain1.ndx -od
   dihed12

   This gives me the distribution at t=800 ps . What i
really want
   is to see the dihedral distribution at all time steps
(after 800
   ps) in one go, and may be do some averaging later. Is there a
   straight forward way to do this. I can imagine that i could
   write a script file that could do this but then i dont
want to
   deal with a lot of files, i rather want everything to be
saved
   in a single file with multiple columns. Could someone
suggest a
   trick for this?


   The first paragraph of g_angle -h suggests there's an option
where
   "the first graph is the average, the rest are the individual
   angles." Does this work?


   Mark
   --gmx-users mailing listgmx-users@gromacs.org

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at http://www.gromacs.org/search before
   posting!
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey 
Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all

output is

# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title "Dihedral Distribution: C34_C36_C37_C38"
@xaxis  label "Degrees"
@yaxis  label ""
@TYPE xy
@subtitle "average angle: 9.87432\So\N"
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
  -1800.015625
  -1790.011719
  -1780.015625
  -1770.00
  -1760.035156
  -1750.031250
  -1740.019531
  -1730.019531
  -1720.023438
  -1710.015625
  -1700.015625

I did not include the distribution for rest of the angles.

The second column is the fractional distribution of dihedrals with the
corresponding angle in the 1st column.

The distribution is averaged over time t = 800ps and 802 ps snapshots. I
checked this part.

Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> It does seem that the -all option averages the distributions. The thing is
>> i was confused with "the first graph is the average, the rest are the
>> individual angles." because when i tried it previously i only found 2
>> columns which were angle and distribution.
>>
>> But now i checked again explicitly by doing few more g_angle commands and
>> it seems that -all does do what i wanted to do. I still dont know what the
>> "rest are the individual angles" means.
>>
>
> I haven't ever used it, but would have expected the output to be along the
> lines of
>
> Time "Average over all angles" Angle-1 Angle-2 ...
> 1  234   23  345
> 2  123   234 232
> 2  223   ...
> 3  323
>
> What output do you get and what seems wrong to you?
>
> Mark
>
>  On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi everyone,
>>
>>I am trying to analyze dihedrals of molecules after a
>>simulation. I am able to calculate dihedral distribution at ant
>>particular time using g
>>-angle and proper group using
>>
>>g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od
>>dihed12
>>
>>This gives me the distribution at t=800 ps . What i really want
>>is to see the dihedral distribution at all time steps (after 800
>>ps) in one go, and may be do some averaging later. Is there a
>>straight forward way to do this. I can imagine that i could
>>write a script file that could do this but then i dont want to
>>deal with a lot of files, i rather want everything to be saved
>>in a single file with multiple columns. Could someone suggest a
>>trick for this?
>>
>>
>>The first paragraph of g_angle -h suggests there's an option where
>>"the first graph is the average, the rest are the individual
>>angles." Does this work?
>>
>>
>>Mark
>>--gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the www
>>interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>  --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Mark Abraham 

Amit Choubey wrote:

Hi Mark,

It does seem that the -all option averages the distributions. 
The thing is i was confused with "the first graph is the average, the 
rest are the individual angles." because when i tried it previously i 
only found 2 columns which were angle and distribution.


But now i checked again explicitly by doing few more g_angle commands 
and it seems that -all does do what i wanted to do. I still dont know 
what the "rest are the individual angles" means. 


I haven't ever used it, but would have expected the output to be along 
the lines of


Time "Average over all angles" Angle-1 Angle-2 ...
1  234   23  345
2  123   234 232
2  223   ...
3  323

What output do you get and what seems wrong to you?

Mark

On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham > wrote:


Amit Choubey wrote:

Hi everyone,

I am trying to analyze dihedrals of molecules after a
simulation. I am able to calculate dihedral distribution at ant
particular time using g
-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od
dihed12

This gives me the distribution at t=800 ps . What i really want
is to see the dihedral distribution at all time steps (after 800
ps) in one go, and may be do some averaging later. Is there a
straight forward way to do this. I can imagine that i could
write a script file that could do this but then i dont want to
deal with a lot of files, i rather want everything to be saved
in a single file with multiple columns. Could someone suggest a
trick for this?


The first paragraph of g_angle -h suggests there's an option where
"the first graph is the average, the rest are the individual
angles." Does this work?


Mark
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey 
Hi Mark,

It does seem that the -all option averages the distributions.
The thing is i was confused with "the first graph is the average, the rest
are the individual angles." because when i tried it previously i only found
2 columns which were angle and distribution.

But now i checked again explicitly by doing few more g_angle commands and it
seems that -all does do what i wanted to do. I still dont know what the
"rest are the individual angles" means.



Thank you,
Amit






On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi everyone,
>>
>> I am trying to analyze dihedrals of molecules after a simulation. I am
>> able to calculate dihedral distribution at ant particular time using g
>> -angle and proper group using
>>
>> g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12
>>
>> This gives me the distribution at t=800 ps . What i really want is to see
>> the dihedral distribution at all time steps (after 800 ps) in one go, and
>> may be do some averaging later. Is there a straight forward way to do this.
>> I can imagine that i could write a script file that could do this but then i
>> dont want to deal with a lot of files, i rather want everything to be saved
>> in a single file with multiple columns. Could someone suggest a trick for
>> this?
>>
>
> The first paragraph of g_angle -h suggests there's an option where "the
> first graph is the average, the rest are the individual angles." Does this
> work?
>
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] doing averages using g_angle

2009-12-01 Thread Mark Abraham 

Amit Choubey wrote:

Hi everyone,

I am trying to analyze dihedrals of molecules after a simulation. I am 
able to calculate dihedral distribution at ant particular time using g

-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12

This gives me the distribution at t=800 ps . What i really want is to 
see the dihedral distribution at all time steps (after 800 ps) in one 
go, and may be do some averaging later. Is there a straight forward way 
to do this. I can imagine that i could write a script file that could do 
this but then i dont want to deal with a lot of files, i rather want 
everything to be saved in a single file with multiple columns. Could 
someone suggest a trick for this?


The first paragraph of g_angle -h suggests there's an option where "the 
first graph is the average, the rest are the individual angles." Does 
this work?


Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] doing averages using g_angle

2009-12-01 Thread Amit Choubey 
Hi everyone,

I am trying to analyze dihedrals of molecules after a simulation. I am able
to calculate dihedral distribution at ant particular time using g
-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12

This gives me the distribution at t=800 ps . What i really want is to see
the dihedral distribution at all time steps (after 800 ps) in one go, and
may be do some averaging later. Is there a straight forward way to do this.
I can imagine that i could write a script file that could do this but then i
dont want to deal with a lot of files, i rather want everything to be saved
in a single file with multiple columns. Could someone suggest a trick for
this?

Thank you,
Amit
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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