The run looks fine to me. Why exactly do you think it's not reading
all of your files? Do you have more than 8 replicas?
-Dan
On Wed, Mar 15, 2017 at 8:13 AM, Ingvild Isaksen
<ingvild.isaksen.nmbu.no> wrote:
> Dear Amber users
>
> I’ve just started running pH replica exchange with Amber 16, but I have problems with the reconstruction of the trajectory files.
>
> This is my cpptraj script when I’m trying to extract data for pH 4.5:
>
>
>
> #!/bin/bash
>
> parm new_radii_prmtop
>
> trajin mdcrd.pH.000 remdtraj remdtrajtemp 4.5
>
> trajout fixed.mdcrd.4.5
>
> go
>
>
> And this is what I get when I try to run it:
>
>
> CPPTRAJ: Trajectory Analysis. V16.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> | Date/time: 03/15/17 11:20:23
> | Available memory: 154.980 MB
>
> INPUT: Reading input from 'reconstructing_traj.cpptraj'
> [parm new_radii_prmtop]
> Reading 'new_radii_prmtop' as Amber Topology
> [trajin mdcrd.pH.000 remdtraj remdtrajtemp 4.5]
> Found 8 replicas.
> Reading 'mdcrd.pH.000' as Amber NetCDF
> [trajout fixed.mdcrd.4.5]
> Warning: Format not specified and extension '.5' not recognized. Defaulting to Amber Trajectory.
> Writing 'fixed.mdcrd.4.5' as Amber Trajectory
> [go]
> ---------- RUN BEGIN -------------------------------------------------
>
> PARAMETER FILES (1 total):
> 0: new_radii_prmtop, 39702 atoms, 12475 res, box: Orthogonal, 12289 mol, 12275 solvent
>
> INPUT TRAJECTORIES (1 total):
> 0: REMD trajectories (8 total), lowest replica 'mdcrd.pH.000' (reading 5000 of 5000)
> Looking for frames at 4.50 K
> Coordinate processing will occur on 5000 frames.
>
> OUTPUT TRAJECTORIES (1 total):
> 'fixed.mdcrd.4.5' (5000 frames) is an AMBER trajectory
>
> BEGIN TRAJECTORY PROCESSING:
> ----- mdcrd.pH.000 (1-5000, 1) -----
> 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
>
> Read 5000 frames and processed 5000 frames.
> TIME: Avg. throughput= 15.3555 frames / second.
>
> ACTION OUTPUT:
>
> RUN TIMING:
> TIME: Init : 0.0000 s ( 0.00%)
> TIME: Trajectory Process : 325.6154 s ( 99.88%)
> TIME: Action Post : 0.0000 s ( 0.00%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0017 s ( 0.00%)
> TIME: Other : 0.3804 s ( 0.00%)
> TIME: Run Total 325.9976 s
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 326.1784 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.
>
>
> To me it seems like it is not able to read all my files, but I am quite new to this so I haven’t been able to figure out how to fixed it myself.
>
> This is the input I’ve used when running the jobs, with changing the solvph from 4.0 to 7.5:
>
>
> prod 2bem
> &cntrl
> ig=-1
> iwrap =1
> imin=0,irest=1,ntx=5,
> nstlim=1000,dt=0.002,
> numexchg=50000,
> ntc=2,ntf=2,
> cut=12, ntb=1, ntp=0, tautp=10.0,
> ntpr=1000, ntwx=10000, ntwr=10000,
> ntt=1,
> temp0=300.0,
> tol=1.0e-8,jfastw=0,
> ntr=1, restraintmask = ':1,108,172 & !.H=',
> restraint_wt=1.0,
> saltcon=0.1, icnstph=2, ntcnstph=100, ntrelax=200,
> solvph=4.5,
> /
> &ewald
> dsum_tol=1.0e-6,
> order=4, skinnb=2.0, vdwmeth=1,
> /
>
>
>
> I’ve checked the replica exchange log file and to me it looks like the pH swaps are going well, it look like the ones I’ve found in tutorials.
>
> I hope someone can help me with what I am doing wrong.
>
> Thanks in advance for all help!
>
>
> Best regards,
> Ingvild Isaksen
> _______________________________________________
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> AMBER.ambermd.org
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Mar 15 2017 - 06:30:03 PDT
