Dear Dan,
Thank you so much for the help and explanation! This will help a lot in further use of cpptraj.
- Ingvild
> On 15 Mar 2017, at 15:17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> The key message is here:
>
> INPUT TRAJECTORIES (1 total):
> 0: REMD trajectories (8 total), lowest replica 'mdcrd.pH.000'
> (reading 5000 of 5000)
>
> CPPTRAJ is letting you know it found 8 replica trajectories but only
> shows the lowest one for the sake of brevity. If you put a 'debug
> trajin 1' (or greater than 1) before your 'trajin' command CPPTRAJ
> will actually print all of the trajectories found. If for some reason
> CPPTRAJ missed a trajectory there would likely have been an error
> during trajectory processing since it would probably encounter a frame
> where it couldn't find your target pH. Let me know if you have more
> questions.
>
> -Dan
>
>
> On Wed, Mar 15, 2017 at 9:42 AM, Ingvild Isaksen
> <ingvild.isaksen.nmbu.no> wrote:
>> Thanks for your answer Dan,
>>
>> To me it only looks like it only reads through the first of my trajectory files, the one called “mdcrd.pH.000”, not the rest of them, because that’s what I can see form the cpptraj run and because I have 5000 frames for each pH, not in total for all the jobs.
>>
>> But I don’t know how the output from cpptraj is supposed to look like, so if you think it looks fine I’ll trust that?
>>
>> - Ingvild
>>
>>
>>> On 15 Mar 2017, at 14:15, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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Received on Wed Mar 15 2017 - 07:30:04 PDT
