[gmx-users] Regarding inter helical distance using g_bundle

[bipin singh]

Thanks for the suggestion. I will try that.

On Tue, Nov 29, 2011 at 19:33, Gianluca Santoni <gianluca.santoni at ibs.fr> wrote:
> On 11/29/11 2:10 PM, bipin singh wrote:
>>
>> Hello,
>>
>> I want to calculate inter helical distance between two helices using
>> g_bundle. As mentioned in the manual that
>> "g_bundle reads two index groups and divides both of them in -na
>> parts. The centers of mass of these parts define
>> the tops and bottoms of the axes".
>> Please suggest me out of two possible options given below which one is
>> the correct way of defining two index groups for calculating
>> inter helical distance :
>>
>> (1) Atom1(CA) and Atom3(CA) in one index and Atom2 and Atom4 in another
>> index
>> (2) Atom1(CA) and Atom2(CA) in one index and Atom3 and Atom4 in another
>> index
>>
>>
>> For reference I am sending the link of figure with above Atom labels.
>>
>> http://researchweb.iiit.ac.in/~bipin.singh/helix.html
>>
>> Please have a look at the figure and provide your suggestions.
>>
>>
>> -----------------------
>> Regards,
>> Bipin Singh
>
> I think g_dist is a easier choice.
>
>
> --
> Gianluca Santoni,
> Institut de Biologie Structurale
> 41 rue Horowitz
> Grenoble
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-- 
-----------------------
Regards,
Bipin Singh