[gmx-users] how to make index of a micelle

[Giuseppe R Del Sorbo]

The micelle contains all the SDS molecules in the system and it's super 
simple at this point because you are right, the SDS molecules is a 
default group.

I thought I should have specified more details.

Ok thanks a lot.
Best,

Giuseppe



Il 2019-11-18 18:14 Justin Lemkul ha scritto:
> On 11/18/19 12:13 PM, Giuseppe R Del Sorbo wrote:
>> Dear Justin,
>> 
>> I want to make an index for the micelle, made od 60 molecules of SDS.
>> 
> 
> So, if I understand correctly, the SDS micelle does not contain all of
> the SDS molecules in the system? That was not clear in your original
> email. If that's the case, the only option is to specify the residue
> numbers individually or to use gmx select with a geometric criterion
> for the spatial coordinates that the micelle occupies. See "gmx help
> selections" for examples.
> 
> -Justin
> 
>> Thanks for the email.
>> 
>> Best,
>> 
>> Giuseppe
>> 
>> 
>> Il 2019-11-18 18:09 Justin Lemkul ha scritto:
>>> On 11/18/19 11:43 AM, Giuseppe R Del Sorbo wrote:
>>>> Dear all,
>>>> 
>>>> In my simulation I have a lysine + micelle of SDS.
>>>> 
>>>> In the analysis, I want to find the spherical radial distribution 
>>>> functions of methyl groups around the center of mass of the micelle.
>>>> 
>>>> I Know how to make the index for the methyl group, but how can I 
>>>> make an index for the micelle?
>>>> 
>>> 
>>> The SDS molecules should already be a default group in the list of
>>> available selections. You shouldn't even need a custom group for it.
>>> 
>>> -Justin
>>> 
>>> -- ==================================================
>>> 
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Office: 301 Fralin Hall
>>> Lab: 303 Engel Hall
>>> 
>>> Virginia Tech Department of Biochemistry
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>> 
>>> jalemkul at vt.edu | (540) 231-3129
>>> http://www.thelemkullab.com
>>> 
>>> ==================================================
> 
> --
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
> 
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
> 
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
> 
> ==================================================