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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--
-------------------------
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 Mon Sep 19 2016 - 07:30:03 PDT
