[gmx-users] plot of mutual orienatation

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> hey Justin,
>  I tried to plot between the groups are planar. But still its giving me
> same error
> 
>  mk_angndx -s 3.tpr -n angle.ndx -type angle (COmmand used for  angle.ndx
> file)
> 
> g_sgangle -f 3.xtc -n angle.ndx  -s 3.tpr -oa test.xvg
> 
> Fatal error: Something wrong with contents of index file.
> 

My previous reply is still applicable.  To do the analysis you want, you may 
have to (by hand) define custom index groups (see the points I raised below). 
The requirements for proper index file content are spelled out in the g_sgangle 
help information and the manual.

-Justin

> Nilesh
> 
> On Fri, December 11, 2009 3:03 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> I tried to to run g_sgangle.
>>> g_sgangle -f 3.xtc -n ac128-no.ndx -s 3.tpr -od test.xvg
>>>
>>> But its giving me following error
>>> Fatal error: Something wrong with contents of index file.
>>>
>>>
>>> I have ploted the rdf with same index file.
>>> Can you tell me where is the problem
>>>
>>>
>> The help information printed by g_sgangle describes the exact
>> requirements.  You may or may not be able to get what you want.  Is the
>> angle between the glucose ring and your 5-membered ring something that is
>> easily described?  Glucose is not planar, so unless you get somewhat
>> creative with the atoms used to describe its ring system, it may not be
>> possible to calculate such an angle.
>>
>> -Justin
>>
>>
>>> Nilesh
>>>
>>>
>>> On Fri, December 11, 2009 2:03 pm, Justin A. Lemkul wrote:
>>>
>>>
>>>> Nilesh Dhumal wrote:
>>>>
>>>>
>>>>> Hey All,
>>>>> I am trying to analyze the results of my simulation. I have used the
>>>>>  ionic liquid as a solvent which have five member ring. I have a
>>>>> glucose molecule surrounded by ionic liquids. I want to see to plot
>>>>> a angle between the center of mass of glucose and center of five
>>>>> member ring. How can I plot
>>>>> the angle between the center of mass of five member sing sothat I
>>>>> can study of orientation of ionic liquids in presence and absence of
>>>>>  glucose. I have run the simulation only of ionic liquids. I tried
>>>>> with g_angle.
>>>>>
>>>> Try g_sgangle.
>>>>
>>>>
>>>>
>>>> -Justin
>>>>
>>>>
>>>>
>>>>> Nilesh
>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>>
>>>>
>>>> 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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>>>>
>>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> 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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>>
>>
> 
> 
> 

-- 
========================================

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

========================================