[gmx-users] making index file

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 26 18:45:19 CEST 2010

----- Original Message -----
From: Moeed <lecielll at googlemail.com>
Date: Friday, August 27, 2010 2:21
Subject: [gmx-users] making index file
To: gmx-users at gromacs.org

> Hello Justin,
> Please let me explain my naive procedure to make index file so that you can make comment. I have created the top file for a single solvent molecule. Then removed [system] , [molecule] directives as well as "#ffgmx.itp". The [molecule type] is named 'solvent''. I got a sample itp file from a tutorial and then copied the contents of this modified top file into the file with itp extention and named it solvent.itp. Then I # included this itp file in solute. top file and based on  solvated gro file added "solvent 1000" in [molecule] directive of solute.top. solvated gro contains residues a,b,c for solute and 'SOL' for the solvent.

That all sounds quite sensible, assuming your solvent is not water.

> then I issue the command : make_ndx -f solvated.gro -o solvated.ndx which lists the residues :
> 0 System              : 30350 atoms
>   1 a                :    10 atoms
>   2 b                 :   330 atoms
>   3 c              :     10 atoms
>   4 SOL                 : 30000 atoms
> I am not getting my default groups according to [moleculetype]. Am I missing sth?  That I am only getting system index group is becase I am only using user defined residues?

The default index groups rely on the residue names being looked up in a database of residue types (IIRC in share/top/aminoacids.dat). You'd have to tweak that for it to work in your case.

> > r1|r2|r3    
> Merged two groups with OR: 
> Merged two groups with OR: 
>   5 r_1_r_2_r_3         :   
> is giving me 
> different directives for system, a, b, c, and SOL and one for 
>  r_1_r_2_r_3 in  solvated.ndx. I dont see what the last one is for?!

That's the one you created. You merged residues 1, 2 and 3 into one group. However you want to merge whole groups, so you want "1 | 2 | 3".

> Residues a, b and c belong to solute and should form one group since I want to get interaction energy 

Maybe residues are equivalent to molecules in your case, but I suspect the above comment indicates at least some confusion somewhere. A group can have many molecules which can have many residues. Or one molecule with one residue. Or some random set of atoms. You choose :-)

> between solute and solvent. How can I create these two groups (to be included in mdp file energy groups ). I searched the manual and archive list but never found such details of creating index files. It seems it is something that everyone knows! :) Please help me.. thanks.

 make_ndx has a tiny help facility which is a useful reminder of how to do some things. Even using it to write out the [ System ] group to an index file, and then manually making a [ Solute ] group from that in a text editor is really not hard (hint: it should probably have the numbers 1 to 350 and nothing else)


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