The essential dynamics method (PROTEINS 17(4), p. 412-425) is able to filter out large correlated motions in the simulated system which occured during the simulation from uninteresting local motions (mostly vibrations).
The method is usually applied in three steps. These steps can be done separately, by calling WEDTRA, WEDEIG and WEDPRJ respectively. At each step, WHAT IF will ask the user a number of questions, after which an input file for the program which contains all input parameters and names of input/output files will appear in an editor on the screen. The user can check if each parameter is correct and when the editor is quit, WHAT IF will run the appropriate program. Output of the three steps can be analysed by calling ANWTRA, ANWEIG and ANWPRJ respectively.
It is also possible to call WEDALL, which will cause WHAT IF to ask only a couple of questions beforehand, and then runs WEDTRA, WEDEIG and WEDPRJ subsequently, after which the results of each step can be analyzed.
0 = select all atoms 1 = select only alpha carbon atoms 2 = select alpha carbon atoms and geometrical centers of the side chains. 3 = select alpha carbon atoms and terminal atoms of the side chains. 4 = select the backbone N,CA,C atoms 5 = select all backbone atoms (N,NH,CA,C,CO) NOTE:There is no side chain on glycine residues, not even an explicit hydrogen in the GROMOS force field. Therefore, for the geometrical center and the terminal atom of the sidechain of a glycine, a virtual position is constructed from the position of the backbone nitrogen, the alpha carbon and the carbonyl carbon atom.
0 = don't print plots, only show them on the screen
1 = make ps files and print the plots (using the command in the cconfi.fig
file)
When starting WEDTRA, WHAT IF will prompt the user for a couple of things:
-a GROMOS coordinate file. This file should contain exactly the same number of atoms as the trajectory that is to be analyzed, and is used for checking how many atoms of each kind (e.g. protein(s), ions, drugs,solvent) are present in the system. Non-zero box lengths at the end of this file cause the program to assume that a simulation with periodic boundary conditions was performed. -the first trajectory filename. -the second trajectory filename. This may be the same as the first trajectory filename. If the name of the first trajectory file contains the number X and the last trajectory file name contains the number Y, then all files from X till Y are taken into account. The program will inspect the format of the trajectory file by the extention. Currently, the GROMOS ASCII, compressed GROMOS ASCII (.Z) and the portable xdr (.xtc, .XTC) formats are suported. Output trajectories are in the xdr format. -for each group that WHAT IF found in the coordinate file, it will ask the user whether it should be included in the analysis or not. In case of a protein, a further selection can be made using WEDSEL (see above).After this, the input file for the program WEDTRA will appear in an editor on the screen. The user may want to check if all paramaters are correct, and changes can be made if necessary. The input file should in principle be self-explanatory.
NOTE:By default, WEDTRA uses the GROMOS coordinate file given on line 1 of the input file also as the reference frame. If this is not the structure on which you want to superpose all frames, you should manually alter the REF parameter in the WEDTRA input file.
WEDTRA requires the following input: -a GROMOS coordinate file containing the same number of atoms as the input trajectory. -a (set of) trajectory file(s). The names of both files must be specified on the WHAT IF prompt.
WEDTRA produces the following output: -a fitted trajectory file (one file, containing all frames) (WEDTRA.XTC, this trajectory can be visualized using the options in the WHAT IF TRAMOV menu). -a GROMOS coordinate file containing the average positions of all selected atoms, WEDTRA.GRO. -a file containing the rms deviation of all fitted frames with respect to the reference frame (WEDTRA.RMS, can be visualized by calling ANWTRA).
Upon calling WEDEIG, WHAT IF will inspect if WEDTRA has already been run in the same directory. If not, WEDEIG will prompt for the name of the input trajectory file, otherwise WHAT IF will by default take the trajectory file generated by WEDTRA (WEDTRA.XTC).
Like with WEDTRA, the inputfile for WEDEIG will appear in an editor on the screen and changes can be made if necessary.
WEDEIG requires the following input: -a single file containing a trajectory file, of which the frames are superimposed onto a single reference structure. Usually, this will be WEDTRA.XTC, generated by WEDTRA.
WEDEIG produces the following output: -a file containing the average positions of the fitted input trajectory in GROMOS trajectory format (WEDEIG.AVP). -a file containing the eigenvalues of the built covariance matrix. (WEDEIG.VAL, this file can be visualized by calling ANWEIG). -a file containing the eigenvectors of the built covariance matrix (WEDEIG.VEC). -files containing 'atomic' eigenvector components (WEDEIG.CMP1 till WEDEIG.CMP10, these files can be visualized by calling ANWEIG). -a file containing the eigenvalues in a cumulative, normalized way. (WEDEIG.CFL, this file can be visualized by calling ANWEIG).
WHAT IF will try to deduce information about the system to be analyzed from the previous steps you took (for instance running WEDTRA or WEDEIG) to prevent having to ask the same questions again.
Like with WEDTRA and WEDEIG, an input file for WEDPRJ will appear in an editor on the screen and changes can be made if necessary. At the end of this file, the indices of the eigenvectors onto which projections are to be made are listed. WHAT IF will by default put the first ten, the twentieth, the fiftieth and the hundredth eigenvector in this list. If another selection is wanted, the list can be altered in the editor.
WEDPRJ requires the following input: -a GROMOS coordinate file containing information about the system that is analyzed. It is suggested that the output average position file produced by WEDTRA is taken (WEDTRA.GRO). -a file containing the input trajectory (portable xdr format) of which the frames will be projected onto selected eigenvectors. Usually, the file WEDTRA.XTC, generated by WEDTRA, will be used here. -a file containing eigenvectors (WEDEIG.VEC). -a file containing the average positions (GROMOS trajectory file format) of the atoms in the input trajectory (WEDEIG.AVP). Notice that from this file the average positions are read, and not from WEDTRA.GRO.
WEDPRJ produces the following output: -files containing projections onto selected eigenvectors (WEDPRJ.PRJ*, these can be visualized by calling ANWPRJ). -files containing the distributions of the projections along selected eigenvectors (WEDPRJ.DIS*, these can be visualized by calling ANWPRJ). -a file containing correlation coefficients between the distributions of the projections of the input trajectory onto selected eigenvectors and corresponding ideal Gaussian distributions (WEDPRJ.CCF, this file can be visualized by calling ANWPRJ). -files containing trajectories (portable xdr trajectory format) of the motion along the first six eigenvectors (WEDPRJ.XTC*, WEDPRJ_A.XTC*, these trajectories can be visualized by using the options in the WHAT IF TRAMOV menu. The WEDPRJ.XTC* files represent the motion along the six eigenvectors with highest eigenvelues in time, the WEDPRJ_A.XTC files represent artificial motions between the minimal and maximal projection along the six eigenvectors with highest eigenvalues). -files containing the coordinates (GROMOS coordinate file format) of the minimum and maximum projections onto the first six eigenvectors translated into cartesian space (WEDPRJ.GRO_MIN*, WEDPRJ.GRO_MAX*, these files can be visualized by WHAT IF).