Manipulate dcd files in the trajectory analysis tools

In this page, we explain how to manipulate single and multiple DCD files in the GENESIS trajectory analysis tool sets. We assume that we have five dcd files: run1.dcd, run2.dcd, run3.dcd, run4.dcd, and run5.dcd, each of which contains 1000, 1000, 5000, 2500, and 2500 snapshots, respectively. For example, run1.dcd was obtained from the following the MD simulation:

[OUTPUT]
dcdfile = run1.dcd         # DCD file

[DYNAMICS]
integrator       = LEAP    # [LEAP,VVER]
nsteps           = 50000   # number of MD steps
timestep         = 0.002   # timestep (ps)
eneout_period    = 50      # energy output period
crdout_period    = 50      # coordinates output period
nbupdate_period  = 10      # nonbond update period

We show some examples of the [TRAJECTORY] section in the control file of the analysis tools.


Case 1: Analyze run1.dcd

In this case, we set md_step1 and mdout_period1 in the [TRAJECTORY] section to be nsteps and crdout_period in the [DYNAMICS] section of the MD control file. Because mdout_perid1 = ana_period1, all 1,000 snapshots are analyzed. If we specify ana_period1 = 100, snapshots are analyzed every 2 steps, namely, 500 snapshots are analyzed.

[TRAJECTORY]
trjfile1      = run1.dcd
md_step1      = 50000
mdout_period1 = 50        
ana_period1   = 50
repeat1       = 1
trj_format    = DCD
trj_type      = COOR+BOX     

Case 2: Analyze run1.dcd 
(same with Case 1)

This is same with Case 1. All 1,000 snapshots in the DCD file are analyzed. If we specify ana_period1 = 2, snapshots are analyzed every 2 steps, namely, 500 snapshots are analyzed.

[TRAJECTORY]
trjfile1      = run1.dcd
md_step1      = 1000
mdout_period1 = 1        
ana_period1   = 1
repeat1       = 1
trj_format    = DCD
trj_type      = COOR+BOX         

Case 3: Analyze run1.dcd and run2.dcd sequentially

In this control file, we analyze run1.dcd and run2.dcd sequentially:

[TRAJECTORY]
trjfile1      = run1.dcd
trjfile2      = run2.dcd
md_step1      = 1000
mdout_period1 = 1        
ana_period1   = 1      
md_step2      = 1000
mdout_period2 = 1        
ana_period2   = 1      
repeat1       = 1
repeat2       = 1
trj_format    = DCD 
trj_type      = COOR+BOX 

Because run1.dcd and run2.dcd contain same number of snapshots, we can set repeat1 = 2, and omit md_srtep2, mdout_period2, ana_period2, and repeat2:

[TRAJECTORY]
trjfile1      = run1.dcd
trjfile2      = run2.dcd
md_step1      = 1000
mdout_period1 = 1        
ana_period1   = 1      
repeat1       = 2           # for trjfile1 and trjfile2
trj_format    = DCD
trj_type      = COOR+BOX 

Case 4: Analyze 
run1.dcd to run5.dcd sequentially

If we analyze multiple DCD files with different number of snapshots, we should combine the above rules. Please, note that the index of the parameters (md_step, mdout_period, ana_period, and repeat) should be sequential from 1 to n (Do not skip any number).

[TRAJECTORY]
trjfile1      = run1.dcd
trjfile2      = run2.dcd
trjfile3      = run3.dcd
trjfile4      = run4.dcd
trjfile5      = run5.dcd
md_step1      = 1000
mdout_period1 = 1        
ana_period1   = 1      
md_step2      = 5000
mdout_period2 = 1        
ana_period2   = 1      
md_step3      = 2500
mdout_period3 = 1        
ana_period3   = 1      
repeat1       = 2          # for trjfile1 and trjfile2
repeat2       = 1          # for trjfile3
repeat3       = 2          # for trjfile4 and trjfile5
trj_format    = DCD
trj_type      = COOR+BOX