[gmx-users] problem with index file

[Justin A. Lemkul]

Moeed wrote:
> Hello,
> 
> I am trying to create an index file to get interaction energies between 
> hexane (C6H14, 20atoms) molecules (interaction energy between two hexane 
> molecules) I have 125 hexane molecules in my system. Please help me 
> figure out what the problem is.
> 
> make_ndx -f Hexane-Stack125.gro -o index.ndx
> 
> what I get from this command line is:
> 
> ************************************************
> 
> Reading structure file
> Going to read 0 old index file(s)
> Analysing residue names:
> Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
> There are:   125      OTHER residues
> There are:     0    PROTEIN residues
> There are:     0        DNA residues
> Analysing Other...
> 
>   0 System              :  2500 atoms
>   1 HEX                 :  2500 atoms
> 
>  nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
>  'a': atom        &   'del' nr         'splitres' nr   'l': list residues
>  't': atom type   |   'keep' nr        'splitat' nr    'h': help
>  'r': residue         'res' nr         'chain' char
>  "name": group        'case': case sensitive           'q': save and quit
> 
> **********************************************************************************
> 
> 1- Can you please help me understand what these mean? I just typed in 
> "q" and exit.
> 

Doing this serves no purpose whatsoever.  If you're keeping the default groups 
that are already generated, there is no need for an index file.  See the last 
line on this page:

http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups

<snip>

> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: readir.c, line: 1007
> 
> Fatal error:
> Group Hexane not found in indexfile.
> Maybe you have non-default goups in your mdp file, while not using the 
> '-n' option of grompp.
> In that case use the '-n' option.
> 
> -------------------------------------------------------
> 
> mdp file:
> 
> 
> title               =  Hexane
> cpp                 =  /lib/cpp
> ;define              =  -DFLEX_SPC    ; This define statement is 
> completely irrelevant if you're not dealing with water.
> constraints         =  all-bonds
> integrator          =  steep
> dt                  =  0.002    ; ps !
> nsteps              =  200
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  1000.0
> emstep              =  0.01
> 
> energygrps          =  Hexane Hexane
> 

"Hexane" is not a group, but "HEX" is.  Furthermore, you're defining the same 
group twice.  The purpose of energygrps is to specify subsets of your system for 
energy terms to be written.  If your system is comprised of only hexane, there 
is only one group to specify.

<snip>

>2- I have a 
> question here: why the first group is named [system] and the second Hex?

See the link quoted above.

<snip>

> 
> I though maybe I should change the name in brackets. I renamed [system] 
> an d{HEX}to {Hexane]  . I grompped again:
> 

Don't.  If you're naming multiple groups the same thing, then you've badly 
broken the purpose of an index file.  From what I can see, you do not need to be 
using energygrps or index files at all!

<snip>

> Fatal error:
> Atom 1 in multiple Energy Mon. groups (1 and 2)

If the groups are redundant, then this makes sense.

-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

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