[gmx-users] plot of mutual orienatation

[Nilesh Dhumal]

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.

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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