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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jun 11 2015 - 21:00:03 PDT
