Hi,
I have 3 trajectory files which are written for simulations "0-50ns", "50-95ns" and "95-100ns". I want to first link them one to other as a chronological order into one trajectory file which contain "0-100ns". It should be in total 50003 frames in the combined trajectory files. However, when I calculated rmsd based on this combined trajectory, it's recognized as only 40485 frames. Before I use ptraj, it works well, but now I use cpptraj. Not sure if this change makes different. Could anyone help me check? Thank you.
You can find some details as below:
the script I used to combine multiple trajectories:
cpptraj -p ../GKDk5.S.top <<eof
trajin ../GKDk5.50ns.mdcrd
trajin ../GKDk5.100ns.mdcrd
trajin ../GKDk5.100ns+.mdcrd
strip :WAT,Na+,Cl-
trajout ./GKDk5.0-100ns.NoWAT.mdcrd
go
eof
Below is the process of cpptraj and rmsd calculation:
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '../GKDk5.S.top' (1 actions):
0: [strip :WAT,Na+,Cl-]
Stripping 25871 atoms.
Stripped parm: '../GKDk5.S.top', 2679 atoms, 168 res, box: Trunc. Oct., 3 mol
----- GKDk5.50ns.mdcrd (1-25000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- GKDk5.100ns.mdcrd (1-23492, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
----- GKDk5.100ns+.mdcrd (1-1511, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 50003 frames and processed 50003 frames.
TIME: Trajectory processing: 250.3706 s
TIME: Avg. throughput= 199.7160 frames / second.
RMSD script:
cpptraj ../GKDk5.H.top <<eof
trajin ./GKDk5.0-100ns.NoWAT.mdcrd
reference ../GKDk5.H.pdb
rms reference mass out GKDk5.0-100ns.all.rmsd
rms reference mass out GKDk5.0-100ns.CA.rmsd .CA
go
eof
RMSD prcess:
INPUT TRAJECTORIES:
0: 'GKDk5.0-100ns.NoWAT.mdcrd' is an AMBER trajectory, Parm ../GKDk5.H.top (reading 40485 of 40485)
Coordinate processing will occur on 40485 frames.
REFERENCE FRAMES (1 total):
0: '../GKDk5.H.pdb', frame 1
Active reference frame for masks is 0
TIME: Run Initialization took 0.0001 seconds.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM '../GKDk5.H.top' (2 actions):
0: [rms reference mass out GKDk5.0-100ns.all.rmsd ]
Target mask: [*](3309)
1: [rms reference mass out GKDk5.0-100ns.CA.rmsd .CA]
Target mask: [.CA](166)
----- GKDk5.0-100ns.NoWAT.mdcrd (1-40485, 1) -----
Best,
Guowei
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Received on Wed Jun 17 2015 - 14:00:02 PDT
