Are you loading your trajectory into vmd as amber coordinates with periodic
box? What happens if you load the combined traj back into cpptraj?
On Thursday, June 11, 2015, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:
> 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 <javascript:;>>
> 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
> <javascript:;>>
> > 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 <javascript:;>>
> wrote:
> > >
> > > > hi
> > > >
> > > > On Thu, Jun 11, 2015 at 10:48 PM, Soong Jiaxin <
> jiaxinsoong.gmail.com <javascript:;>>
> > > > 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jun 11 2015 - 21:00:05 PDT
