Yes, I know it from VMD. I am puzzled too as the cpptraj's output shows
5000 frames.
On 12 June 2015 at 11:39, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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.
> > > > _______________________________________________
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Received on Thu Jun 11 2015 - 21:00:04 PDT
