[gmx-users] Reference atoms for gmx mdmat and gmx rmsf

[Sampurna Mukherjee]

Hi gmx-users,
                              There are a few things I wanted to know:

   1.  For RMSF calculations, which atoms are used when I am calculating
   RMSF for a group specified in the index?
   2. For gmx mdmat , for 2 protein chains taken together i.e using the
   Protein group ,  "smallest distance between residue pairs" implies the
   smallest distance over the trajectory between say the first and the 15th
   residue.Yes?
   3. Which atoms are being considered for calculation of smallest
   distances?



Regards,
Sampurna