[gmx-users] g_select

[Justin A. Lemkul]

mohammad agha wrote:
> Thanks for your reply, but how can I define residue numbers of one 
> micelle from between 10 micelle that all of them are same and only were 
> differ at the number of monomer in micelle.
> May I know how, please?

Well, now the problem is potentially more complicated.  Two approaches:

1. Using make_ndx, you can create an index file of any micelle if you know all 
of the residue numbers.  Please type "help" at the make_ndx prompt for example 
usage.  It is easy to do.

2. If you do not know which residues comprise the micelle(s) and you don't want 
to figure it out manually (I wouldn't), then you need g_select with some 
geometric criteria.  Again, there is help available (see g_select -h for how to 
invoke help) and search the archives for related posts.

It would be far more efficient for you and for those who might help you if you 
post what you've tried and failed at, rather than leaving us to guess what might 
work.

-Justin

> 
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* mohammad agha <mra_bu at yahoo.com>; Discussion list for GROMACS 
> users <gmx-users at gromacs.org>
> *Sent:* Wednesday, November 30, 2011 7:03 PM
> *Subject:* Re: [gmx-users] g_select
> 
> 
> 
> mohammad agha wrote:
>  > Dear Prof.
>  >
>  > I have a system consists of 10 micelle after production simulation. 
> How can I select a micelle with 92 monomer?
>  > I know that I should use from g_select, but I don't know which 
> argument is proper for me. I also checked -select help in g_select program.
>  > Please help me.
>  >
> 
> If you just need an index group with a single micelle, use make_ndx and 
> choose the residue numbers that comprise the micelle.  g_select can do 
> the same, but this tool is better suited for more complex operations and 
> creation of dynamic indices.
> 
> -Justin
> 
> -- ========================================
> 
> 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
> 
> ========================================
> 
> 

-- 
========================================

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

========================================