hi,
how can you tell the combined traj has only 4989 frames (from vmd?) ? I
only see 5000 frames in the cpptraj's output.
Hai
On Thu, Jun 11, 2015 at 11:29 PM, Soong Jiaxin <jiaxinsoong.gmail.com>
wrote:
> This is the log file for stripping the water and ions. I stripped each of
> the mdcrd file one by one.
>
> CPPTRAJ: Trajectory Analysis. V14.25
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Reading '../Model3_solvated.prmtop' as Amber Topology
> INPUT: Reading Input from STDIN
> [trajin ../Prod1.mdcrd]
> Reading '../Prod1.mdcrd' as Amber Trajectory
> [autoimage]
> AUTOIMAGE: To box center based on center of mass, anchor is first
> molecule.
> [strip :WAT]
> STRIP: Stripping atoms in mask [:WAT]
> [strip :Na+ ]
> STRIP: Stripping atoms in mask [:Na+]
> [trajout Prod1_a_dry.mdcrd ]
> Writing 'Prod1_a_dry.mdcrd' as Amber Trajectory
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: '../Model3_solvated.prmtop', 34928 atoms, 11035 res, box: Orthogonal,
> 10892 mol, 10885 solvent, 1000 frames
>
> INPUT TRAJECTORIES:
> 0: 'Prod1.mdcrd' is an AMBER trajectory, Parm ../Model3_solvated.prmtop
> (Orthogonal box) (reading 1000 of 1000)
> Coordinate processing will occur on 1000 frames.
>
> OUTPUT TRAJECTORIES:
> 'Prod1_a_dry.mdcrd' is an AMBER trajectory, Parm
> ../Model3_solvated.prmtop: Writing 1000 frames (1-Last, 1)
> TIME: Run Initialization took 0.0000 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM '../Model3_solvated.prmtop' (3 actions):
> 0: [autoimage]
> Anchor molecule is 1
> 10891 molecules are mobile.
> 1: [strip :WAT]
> Stripping 32655 atoms.
> Stripped parm: '../Model3_solvated.prmtop', 2273 atoms, 150 res, box:
> Orthogonal, 7 mol
> 2: [strip :Na+ ]
> Stripping 6 atoms.
> Stripped parm: '../Model3_solvated.prmtop', 2267 atoms, 144 res, box:
> Orthogonal, 1 mol
> ----- Prod1.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 1000 frames and processed 1000 frames.
> TIME: Trajectory processing: 26.5565 s
> TIME: Avg. throughput= 37.6556 frames / second.
>
> ACTION OUTPUT:
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 26.6943 seconds.
>
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
>
>
> This is the cpptraj log file for combining the mdcrd files:
>
>
> CPPTRAJ: Trajectory Analysis. V14.25
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Reading 'strip.Model3_solvated.prmtop' as Amber Topology
> INPUT: Reading Input from STDIN
> [trajin Prod1_a_dry.mdcrd]
> Reading 'Prod1_a_dry.mdcrd' as Amber Trajectory
> [trajin Prod2_a_dry.mdcrd]
> Reading 'Prod2_a_dry.mdcrd' as Amber Trajectory
> [trajin Prod3_a_dry.mdcrd]
> Reading 'Prod3_a_dry.mdcrd' as Amber Trajectory
> [trajin Prod4_a_dry.mdcrd]
> Reading 'Prod4_a_dry.mdcrd' as Amber Trajectory
> [trajin Prod5_a_dry.mdcrd]
> Reading 'Prod5_a_dry.mdcrd' as Amber Trajectory
> [trajout allProd_dry.mdcrd]
> Writing 'allProd_dry.mdcrd' as Amber Trajectory
> [go]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES:
> 0: 'strip.Model3_solvated.prmtop', 2267 atoms, 144 res, box: Orthogonal, 1
> mol, 5000 frames
>
> INPUT TRAJECTORIES:
> 0: 'Prod1_a_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> 1: 'Prod2_a_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> 2: 'Prod3_a_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> 3: 'Prod4_a_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> 4: 'Prod5_a_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop (Orthogonal box) (reading 1000 of 1000)
> Coordinate processing will occur on 5000 frames.
>
> OUTPUT TRAJECTORIES:
> 'allProd_dry.mdcrd' is an AMBER trajectory, Parm
> strip.Model3_solvated.prmtop: Writing 5000 frames (1-Last, 1)
> TIME: Run Initialization took 0.0000 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> ----- Prod1_a_dry.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- Prod2_a_dry.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- Prod3_a_dry.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- Prod4_a_dry.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> ----- Prod5_a_dry.mdcrd (1-1000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 5000 frames and processed 5000 frames.
> TIME: Trajectory processing: 32.0629 s
> TIME: Avg. throughput= 155.9433 frames / second.
>
> ACTION OUTPUT:
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 32.0862 seconds.
>
> --------------------------------------------------------------------------------
> To cite CPPTRAJ use:
> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
> Theory Comput., 2013, 9 (7), pp 3084-3095.
>
> My production is 5ns long. The following is the input file which I repeated
> the step for 5 times.
>
> Prod Model3
> &cntrl
> imin=0, ntx=5, irest=1,
> nstlim=500000, dt=0.002,
> ntf=2, ntc=2,
> ntpr=100, ntwx=500,
> cut=8.0, ntb=2,
> ntp=1, ntt=1,
> iwrap=1,
> taup=2.0,
> temp0=300.0, tempi=300.0,
> ig=-1,
> /
>
> On 12 June 2015 at 11:14, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > hi
> >
> > On Thu, Jun 11, 2015 at 10:48 PM, Soong Jiaxin <jiaxinsoong.gmail.com>
> > wrote:
> >
> > > Hi all,
> > >
> > > I'm facing problem with my stripped combined mdcrd files. I found out
> > that
> > > the number of frames has been reduced from 5000 frames to 4989 frames
> > after
> > > stripping the water molecules and ions.
> >
> >
> > can you post the cpptraj's output + your system info, ...?
> >
> >
> > > Other than that, I also discovered
> > > that the size of combined mdcrd files post stripping is 275.6MB.
> However,
> > > the size of combined mdcrd files before stripping is 4.2GB.
> >
> >
> > yes, the size of water-stripped traj should be much smaller.
> >
> >
> > > My concern is
> > > this normal or is it going to affect my result when I used the stripped
> > > files to extract the average structure? How do I solve this problem?
> > >
> > > I'd appreciate any help or comment.
> > >
> > > Vanessa.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Thu Jun 11 2015 - 21:00:03 PDT
