Hi,
I'm not able to reproduce your issue. Also, based on the names of the
files you attached I expected one to be from cpptraj version 16, but
both are from 15 (also they are for difference sets of trajectories) -
are you sure you attached the right output?
-Dan
On Mon, Sep 19, 2016 at 10:12 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Just to be clear, which version gave you the strange result? Was it 15
> and 16 or just 16?
>
> -Dan
>
> On Thu, Sep 15, 2016 at 2:24 AM, <dhanasekar.mbu.iisc.ernet.in> wrote:
>> Hi,
>>
>> I re-ran the analysis to test whether different cpptraj versions were giving
>> rise to these discrepancies.
>>
>> I tested 20ns production run data on 2 systems, one with Ubuntu13 32 bit,
>> cpptraj15.00 (updated recently), and another with Ubuntu14 64-bit, cpptraj16.12.
>>
>> I am attaching data files (.dat) and log files (.log) files for both these
>> runs.
>>
>> As you will see, the 32 bit systems are reporting this sudden jump in RMSD,
>> whereas the 64-bit systems the showing the RMSD to be within 1 and 2 Angstrom(
>> i.e protein seems to be stable )
>> Inspite of upgrading from cpptraj version 14 to 15 (on 32bit machine), I saw
>> the same jumps in RMSD. ( I have attached version14's rmsd.dat file too, check
>> line number 4914-5100, 9914-10100 and 14914-15100 so on and so forth.
>> The rest of the RMSD values are identical for all .dat files(across all
>> platforms), except the frame numbers mentioned above.
>>
>> When viewing these trajectories in VMD, I didnt see any drastic changes either.
>> I didnt get any errors during these cpptraj runs. Also, I made
>> sure that I was using the same data files, prmtop files and .in files.
>>
>> Please guide me about this.
>> What precautions should I take while running cpptraj on 32 bit Ubuntu machines?
>> Help is highly appreciated.
>>
>> BK Dhanasekharan
>>
>>
>>
>>> Hi
>>>
>>> Can you try the most updated cpptraj (ambertools16) and let us know what
>> happens.
>>
>> By the way, are you sure you used identical input?
>> ** yes, we have used identical inputs in all cases.
>>
>> In the first figure, you have 100 ns while in the 2nd one you have 95 ns. Can you
>> attach cpptraj log for 2nd run?
>> ** In the first figure, 100ns data was used.
>> In the 2nd figure, i have used 20ns data (sorry I mislabelled the figure). But
>> we did not get any errors in the log reports.
>>>
>>> Hai
>>>
>>>> On Sep 8, 2016, at 11:05 AM, dhanasekar.mbu.iisc.ernet.in wrote: Hi, I am
>> running prot+ligand simulation for a couple of systems for understanding ligand
>> bound conformational changes. (I have used standard Amber14 protocols for
>>>> setting up the system, minimization, equilibration, etc.)
>>>> I have generated 100ns production run data and am using cpptraj version 14.25
>> for the analysis.
>>>> I had earlier run rmsd calculations for all systems using the following
>> script
>>>> :
>>>> strip :WAT
>>>> strip :Na+
>>>> center :1-250 mass
>>>> autoimage
>>>> rms first out rmsd.dat :1-250.CA
>>>> atomicfluct out Per-res-fluct.dat :1-250 byres
>>>> atomicfluct out CA-fluct.dat .CA byatom
>>>> go
>>>> rmsd was below 2Ã… and system appeared stable.
>>>> I have to re-run rmsd again, and am facing some problems inspite of using
>> same
>>>> crd files, same prmtop file and same rmsd.in file :
>>>> 1) RMSD data shows RMS as high as 25-45Ã… for a selected number of snapshots
>> after an interval of 50 frames. I find this very weird since I used the same
>> data ( crd files) a few days back with the same prmtop file and with the same
>> cpptraj code, but did not see any of this earlier.
>>>> No errors were reported during cpptraj analysis. After data has been
>> generated,
>>>> it looks something like.
>>>> When visualised in VMD, I do not see any drastic changes in the prot
>> structure.
>>>> Everything appears to be OK.
>>>> Is there any way to rectify this ? What seems to be the problem? Is this an
>> imaging issue or have the trajectories become corrupted? If so, please suggest
>>>> remedial measures.
>>>> Thank you.
>>>> Regards,
>>>> B.K. Dhanasekaran
>>>> --
>> --
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>>
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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
--
-------------------------
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 Tue Sep 20 2016 - 08:30:05 PDT
