[gmx-users] g_gyrate

[C. Batistakis]

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.

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. 

I hope know you understand

Many thanks
Chrysostomos




--- Στις Τρίτ., 12/10/10, ο/η Mark Abraham <mark.abraham at anu.edu.au> έγραψε:

Από: Mark Abraham <mark.abraham at anu.edu.au>
Θέμα: Re: [gmx-users] g_gyrate
Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Ημερομηνία: Τρίτη, 12 Οκτώβριος 2010, 13:47

I'm not sure what the problem is. If you want to merge groups to get the radius of gyration over the union of those groups, then you need to use make_ndx on your previous .ndx file to generate such a group.

Mark

----- Original Message -----
From: "C. Batistakis" <cbatiss at yahoo.gr>
Date: Tuesday, October 12, 2010 21:44
Subject: [gmx-users] g_gyrate
To: gromacs <gmx-users at gromacs.org>

> Dear all
> 
> I have the following system. Substrate with 3696 particles and 4 polymer chains with 45 beads/chain.  After typing g_gyrate, I have the following option:
> 
> Group     0 (      System) has  680 elements
> Group     1 (         ZZZ) has   500 elements
> 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 a group:
> 
> Can someone tell me how can I calculate the average radius of gyration  only from the groups 2,3,4,5 of the previous system? 
> 
> Thanks in advance
> Chrysostomos
> 
> 
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