Handle dcd files in the trajectory analysis tools
In this page, we explain how to handle 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
Written by Takaharu Mori@RIKEN Theoretical Molecular Science Laboratory
Aug. 12, 2016