Did you try cpptraj v16 with 32 bit yet?
PS: Please reply to amber mailing list
Hai
On Thu, Sep 15, 2016 at 2:28 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 2Å 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 25-45Å 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
> >> --
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 15 2016 - 07:30:03 PDT
