Afternoon all,
I want to calculate an average RMSD across the timescale of my simulation
by using three independent trajectories as inputs. Currently, cpptraj is
catenating all of the three trajectories when calculating the RMSD. Below
is my input script:
trajin ../1/2fct_WT_nvt-binary.nc
trajin ../2/2fct_WT_nvt-binary.nc
trajin ../3/2fct_WT_nvt-binary.nc
reference ../2fct_WT_npt2.rst
center :1-308
image
rmsd BB :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat
And this is the output:
PARAMETER FILES:
0: '2fct_WT_solv.prmtop', 39040 atoms, 11749 res, box: Orthogonal, 11443
mol, 11408 solvent, 18750 frames
INPUT TRAJECTORIES:
0: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
1: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
2: '2fct_WT_nvt-binary.nc' is a NetCDF AMBER trajectory, Parm
2fct_WT_solv.prmtop (Orthogonal box) (reading 6250 of 6250)
Coordinate processing will occur on 18750 frames.
REFERENCE FRAMES (1 total):
0: '../2fct_WT_npt2.rst', frame 1
Active reference frame for masks is 0
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '2fct_WT_solv.prmtop' (3 actions):
0: [center :1-308]
Mask [:1-308] corresponds to 4783 atoms.
1: [image]
Number of molecules to be imaged is 11443 based on mask '*'
2: [rmsd BB :110.C,CA,N,:229.C,CA,N,:305-308 first mass out rmsd-BB.dat]
Mask [:110.C,CA,N,:229.C,CA,N,:305-308] corresponds to 21 atoms.
Mask [:110.C,CA,N,:229.C,CA,N,:305-308] corresponds to 21 atoms.
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- 2fct_WT_nvt-binary.nc (1-6250, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 18750 frames and processed 18750 frames.
TIME: Trajectory processing: 32.2032 s
TIME: Avg. throughput= 582.2396 frames / second.
ACTION OUTPUT:
DATASETS:
1 data set:
BB "BB" (double, rms), size is 18750
DATAFILES:
rmsd-BB.dat (Standard Data File): BB
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 32.6381 seconds.
--------------------------------------------------------------------------------
,
The output gives the RMSD of my mask over 18750 frames, when what I want is
the average value of the three simulations, which will only give 6250
frames. Any tips or suggestions?
Best,
Hunter
--
Hunter Wilson
Chemistry PhD Student
General Chemistry Teaching Assistant
wils1872.umn.edu
Department of Chemistry
University of Minnesota- Twin Cities
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Received on Mon Jan 14 2019 - 13:30:02 PST
