On 4/21/2011 10:33 AM, Mark Abraham wrote:
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.
Actually, tpbconv has the ability to set the charges of a group in a
.tpr to zero.
Mark
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