[gmx-users] plot of mutual orienatation

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> Hey Justin,
> I have a small query. I have total 128 pairs of ionic liquids. THats why
> most of the group have more that 3 elements.  Now If I manually make the
> groups with 2 or 3 elements (which is really hard and no. groups will be
> more than 1000)then How can I take the average.

Have a look at g_sorient, as well; it may serve you better.

-Justin

> Nilesh
> 
> On Fri, December 11, 2009 9:22 pm, Justin A. Lemkul wrote:
> 
>> 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
>>
>>
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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

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