[gmx-users] gmx sasa

[Sudip Das]

Dear All,

I am using 'gmx_mpi sasa' module as below:

gmx_mpi sasa -f traj_0-100ns.xtc -s topol.tpr -o sasa -or res_sasa -q
surface.pdb -surface -b 50000

Now, surface.pdb file will generate the surface of the selected portion
together with the coordinates of all the atoms present in the protein. Are
the coordinates of all atoms of the protein averaged over the selected
range of trajectory or they are averaged over the range of trajectory
supplied in the .xtc file (as for example, here, I have selected 50-100 ns,
though my .xtc file ranges from 0-100 ns)?
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Thanks in advanced!

Best wishes,
Sudip