[gmx-users] plot of mutual orienatation

[Nilesh Dhumal]

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

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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