[gmx-users] Reference atoms for gmx mdmat and gmx rmsf
e.jjordan12 at gmail.com
Thu May 17 11:35:01 CEST 2018
RMSF is calculated for the atoms or groups you specify in your selection
string. If you say, e.g. "protein and name CA" you will get all C alphas in
the protein(s) in your system. See here
On Thu, May 17, 2018 at 10:18 AM, Sampurna Mukherjee <
sampurnamukherjeebiology at gmail.com> wrote:
> 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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