ETAPA I Arquivo: media.cpptraj # in this file we take the unique trajectory of the simulation and generate a pdb file of the average of the trajectories trajin proteina.mdcrd # cpptraj -i media.cpptraj -p proteina.prmtop autoimage average media.pdb pdb nowrap ETAPA II Arquivo: tira.cpptraj # in this file we create a new unique trajectory starting, for example in this case of structure 1 and saving 1 frame every 60 frames of the whole simulation # in this step we used the reference media.pdb file created in the first step trajin proteina.mdcrd 2500 last 60 reference media.pdb # cpptraj -i tira.cpptraj -p proteina.prmtop autoimage trajout proteina-II.mdcrd netcdf ETAPA III Arquivo: pca-cpu-gpu.cpptraj # in this file we will calculate the vectors for the PCA projection. We have to provide information on the trajectory file, the mask on which type                                                   #  of atom will be calculated -example @CA, on alpha carbon atoms mudancas nas linhas: trajin proteina-II.mdcrd parm rms first @CA # cpptraj -i pca-cpu-gpu.cpptraj crdaction proteina-trajectories rms ref AVG @CA crdaction proteina-trajectories matrix covar \ name cpu-gpu-covar @CA nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask @CA beg 1 end 3 @CA crdframes 1,2500 # In this line, the number of frames 2500 comes from the unique trajectory file created when specifying 2500 last 60 - at the command line of the # file 1.2500 means the first frame to the last of this new single path, so this number # must be checked in the output file when running the file tira.cpptraj hist CPU:1 bins 2500 out cpu-gpu-hist.agr norm name CPU-1 hist CPU:2 bins 2500 out cpu-gpu-hist.agr norm name CPU-2 # 2500 here comes from the trajectories selected in the previous command readdata cpu-gpu-evecs.dat name Evecs # this cpu-gpu-evecs.dat file is that they have the vectors that will be used for the PCA projection in the next step pcmin -2500 pcmax 2500 tmode 1 trajoutmask @CA trajoutfmt netcdf # once again, the number of frames and the mask used are specified, in the case on the @CA ETAPA IV Arquivo: PCA.cpptraj # in this file we will use the file cpu-gpu-evecs.dat created in the previous step in which we will do the projection of the modes of the vectors trajin proteina-II.mdcrd projection modes cpu-gpu-evecs.dat out pca12-ca beg 1 end 3 @CA # cpptraj -i PCA.cpptraj -p proteina.prmtop go Mudança na Etapa II # The change in this step - 2500 last 10 - means that we analyze the RMSD of the protein and verify that the system stabilizes after the                                                                       the first 10 ns of simulation of the production stage, so we discarded the first 2500 corresponding frames. Arquivo: tira.cpptraj trajin proteina.mdcrd 2500 last 10 reference media.pdb autoimage trajout proteina-II.mdcrd netcdf