Hi,
we are working with a protein-ligand system (MHC + peptide). We have
computed radius of gyration using the following command line:
g_gyrate -f File1.xtc -s File2.tpr -n index.ndx -o GYRATE
* File1: refer to concatenated trajectories of our *protein* plus *ligand
*during 8ns simulation.
We choose the *ligand* group to compute the radius of gyration. My questions
are:
1) Which center of mass GROMACS will set: the center of mass of the ligand
or of the protein?
2) If the center of mass is the protein, all the atoms of the ligand are
used for the radius og gyration calculation?
Thanks in advance
--
Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul
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