[gmx-users] g_dipoles + tpbconv

[Nilesh Dhumal]

Hello,

I have a system with a glucose molecule.

I want to calculate the dipole moment of a particular OH in glucose
molecule.I made an index file which have a group containing atoms.

[ O8 ]
  8   18

10 is oxygen no. and 20 is hydroen no.



But, if I try to use g_dipoles to get the dipole moment contribution from 
using following command:

g_dipoles -f 6.trr -s 6.tpr  -n index.ndx -corr mol -nonormalize  -c

I get the following error.

Fatal error:
index[1]=8 does not correspond to the first atom of a molecule

I read on gmx-users mailing list.

http://www.mail-archive.com/gmx-users@gromacs.org/msg40091.html

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. 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.

So I tried

tpbconv -f 6.trr -s 6.tpr -n glu-emi-cl-128-no.ndx -e 6.edr  -o zero.tpr

I got the error

segmentataion fault

How can I solve this problem to calcualte the dipole moment of a bond?

I am using gromacs version 4.0.7.

Thanks

Nilesh