[gmx-users] g_gyrate

[Mark Abraham]

----- Original Message -----
From: "C. Batistakis" <cbatiss at yahoo.gr>
Date: Wednesday, October 13, 2010 1:41
Subject: Re: [gmx-users] g_gyrate
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

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| > Dear Mark
> I will try to be more specific.
> 
> In the case I have 4 chains in a simulation box, by typing g_gyrate -f traj.xtc -s topol.tpr -nmol 4 I take the following:
> 
>  Group     0 (      System) has  180elements
>  Group     1 (         AAA) has    45 elements
>  Group     2 (         BAA) has    45 elements
>  Group     3 (         CAA) has    45 elements
>  Group     4 (         DAA) has    45 elements
> Select group:
> 
> By choosing here the Group 0, GROMACS  calculates the Rg for each chain and then calculates the average Rg.

Here, System is the union of the four other groups. I'm not sure why g_gyrate can tell the chains apart from the group you've chosen. I've never used g_gyrate.

> Now I have the same system but with a substrate. I want to calculate again the average Rg for these 4 chains without taking into acount the substrate. So, how can I select in the following only the 4 chains and find again the average Rg? 
> 
> Group     0 (      System) has  680elements
> Group      1 (         ZZZ)  has    500elements
> Group     2 (         AAA) has    45 elements
> Group     3 (         BAA) has    45 elements
> Group     4 (         CAA) has    45 elements
> Group     5  (         DAA) has    45 elements
> Select group:
> 
> Notice that I don't want to find the Rg over the union of the chains, but the local Rg of each chain and then to take the average. 
 |
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By analogy, if your above description is accurate, you should get the result you want from using make_ndx to make a union of the four polymer chains, and then choosing that group in g_gyrate.

Mark

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