[gmx-users] problem with g_dipoles and index file

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 21 02:38:01 CEST 2011

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.


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