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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Received on Wed Sep 14 2016 - 23:30:02 PDT
