[gmx-users] plot of mutual orienatation

[Nilesh Dhumal]

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.
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
>>>
>>>
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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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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