[gmx-users] plot of mutual orienatation

[Justin A. Lemkul]

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

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