[gmx-users] About g_mdmat function

[Mark Abraham]

Keunwan Park wrote:
> Dear all
> 
> I use index file to make residue group and run g_mdmat function with the
> ndx file.
> 
> For example, the residue groups are composed of 8 residues and the
> program said ...
> --------------------------------------------------------------------------
> Selected 10: 'r_81_r_82_r_83_r_102_r_111_r_149_r_178_r_182'
> There are 182 residues with 100 atoms
> --------------------------------------------------------------------------
> 
> Why the program recognize 182 as a total residue number instead of 8 ?
> PixMap matrix file also show 182 residues.

Were there 182 residues originally?

> How do I draw the matrix file with 8 residues ?

You can use modes of trjconv and tpbconv to make trajectory and run
input files for only this subset of the residues and give those as input
to g_mdmat.

Mark