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
>
> _______________________________________________
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Received on Wed Mar 15 2017 - 07:00:02 PDT
