remd_convert
This tool can manupulate REMD trajectory files as in the crd_convert tool. Since REMD trajectories generated from GENESIS are the “mixture” of trajectories in different temperatures, the user has to sort trajectories by temperatures. Here, we consider that the user specified the following information in the control file of REMD:
[OUTPUT]
logfile = run_rep{}.log
rstfile = run_rep{}.rst
dcdfile = run_rep{}.dcd
remfile = run_rep{}.rem
[REMD]
exchange_period = 1000
type1 = TEMPERATURE
nreplica1 = 8
parameters1 = 300 302 304 306 308 310 312 314
[DYNAMICS]
integrator = LEAP # [LEAP,VVER]
nsteps = 100000 # number of MD steps
timestep = 0.002 # timestep (ps)
eneout_period = 100 # energy output period
crdout_period = 100
An example of remd_convert for this REMD simulation is as follows, where the trajectory at T = 300 is generated. The color means one-to-one correspondence between REMD and remd_convert.
[INPUT] psffile = 2ech.psf # protein structure file reffile = 2ech.pdb # PDB file remfile = run_rep{}.rem # REMD parameter ID file dcdfile = run_rep{}.dcd # DCD file logfile = run_rep{}.log # REMD energy log file [OUTPUT] trjfile = run_par{}.dcd # coordinates sorted by temperature logfile = run_par{}.log # energy log sorted by temperature [SELECTION] group1 = all # selection group 1 [FITTING] fitting_method = NO # [NO,TR,TR+ROT,TR+ZROT,XYTR,XYTR+ZROT] mass_weight = NO # mass-weight is not applied [OPTION] check_only = NO convert_type = PARAMETER # (REPLICA/PARAMETER) num_replicas = 8 # total number of replicas used in the simulation convert_ids = 1 # selected index (empty = all)(example: 1 2 5-10) nsteps = 100000 # nsteps in [DYNAMICS] exchange_period = 1000 # exchange_period in [REMD] crdout_period = 100 # crdout_period in [DYNAMICS] eneout_period = 100 # eneout_period in [DYNAMICS] trjout_format = DCD # (PDB/DCD) trjout_type = COOR+BOX # (COOR/COOR+BOX) trjout_atom = 1 # atom group centering = NO pbc_correct = NO