The RMSF command calculates the final root mean square fluctuations from the data accumulated previously with the AddPos command. Depending on the Unit parameter, the RMS fluctuations are either returned in Angstrom or as B-factors. In the latter case, the B-factors are also transferred to the atoms .

The RMSF of atom i in Angstrom is obtained with the following formula, where j runs over the three cartesian components x, y and z of the atom position vector P, and k runs over the N coordinate sets added with the AddPos command:

The B-factor is obtained with the following conversion factor from the RMSF in [A]:

The complete procedure for obtaining RMSF values is as follows (and implemented as part of the macro md_analyze):

• Load the starting structure as a reference.
• Load a simulation snapshot.
• Superpose it onto the reference structure to remove translational and rotational degrees of freedom.
• Use AddPos to add the current atom positions to the internal calculation table.
• Repeat for all simulation snapshots.
• In the end, use RMSF to calculate the results.

While per-atom fluctations are uniquely defined, fluctuations of larger units (residues, molecules) can be obtained in two ways:

• Calculate the geometric center of each unit and calculate the fluctuation of its position. This operation is performed if the command extension of the AddPos command is not 'Atom'.
• Calculate the per-atom fluctuations and then average the result over all atoms in the unit. This operation is performed if the command extension of the RMSF command is not 'Atom'.

All combinations are possible, e.g. you could add the fluctations of the geometric residue centers with 'AddPosRes' and then obtain the final result as an average over entire molecules with 'RMSFMol'.

Use the Clear command to clear the internal atom position table and start a new round of calculations.

Note that B-factors obtained with this command are typically larger than those found in X-ray structures. First the crystal environment reduces the protein's flexibility, and second crystal structures are usually solved at low temperature.

RMSFAtom Obj 1,Unit=A

Calculate the final root mean square fluctuations in units of Angstrom for the atoms in object 1.

RMSFRes Obj 1,Unit=A

As above, but average the result over the atoms in each residue.

RMSFRes Obj 1,Unit=BFactor

As above, but print the result as B-factors and set the atomic B-factors accordingly.

bflist() = RMSFAtom all,BFactor

Assign the root mean square fluctuations of all atoms to list 'bflist'.