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
>
> _______________________________________________
> 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
Received on Wed Mar 15 2017 - 07:30:02 PDT
