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

Sampurna Mukherjee sampurnamukherjeebiology at gmail.com
Thu May 17 10:18:57 CEST 2018

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
   3. Which atoms are being considered for calculation of smallest


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