[gmx-users] problem with g_dipoles and index file

[Mark Abraham]

On 4/21/2011 10:17 AM, Sanku M wrote:
> Hi,
>   I was trying to calculate the dipole moment of part of my peptide. 
> In other words, if I have a 10-residue peptide, I was interested in 
> calculating the dipole-moment contribution of the backbone. So, I made 
> an index file which have a group containing backbone atoms. But, if I 
> try to use g_dipoles to get the dipole moment contribution from the 
> backbone atoms, using following command:
> g_dipoles  -s  -f  traj -n index.ndx
> I get an error :
> -------------------------------------------------------
> Program g_dipoles_mod_4mpi, VERSION 4.0.5
> Source code file: gmx_dipoles.c, line: 1173
>
> Fatal error:
> index[1]=197 does not correspond to the first atom of a molecule
> -------------------------------------------------------

Calculating a dipole moment of a possibly-charged species requires that 
there be a reference point, which is conventionally the center of mass 
of the molecule. This means all the atoms of the molecule have to be 
known, and g_dipoles assumes the index group consists of whole molecules.

So to do the partition you want, you will need to provide the same 
molecules, but with zero charges on the non-backbone atoms. That will 
mean making a copy of your .top and hacking those charges to zero to 
generate a new such .tpr.

Mark



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