hi,
does *GKDk5.H.top* have the same number of atoms as
*GKDk5.0-100ns.NoWAT.mdcrd* traj?
just make sure / confirm you use correct topology files first.
Hai
On Wed, Jun 17, 2015 at 4:33 PM, Yin, Guowei <guowei_yin.med.unc.edu> wrote:
> 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 - 14:00:03 PDT
