Proteins are a chaotic system, so once a tiny difference exists, it will
compound very very quickly. Therefore, once the simulations diverge
slightly (at step 400) the simulations will become drastically different
after a small amount of time. Both simulations are valid, you don't have to
discard either. You can see similar differences on the same machine using
different compilers as well (sometimes).
In fact, if you start from exactly the same starting point with exactly the
same inputs on the same machine with the same installation, and change the
random seed slightly, the resulting simulations will diverge on the
picosecond timescale. This behavior is to be expected.
All the best,
Jason
On Sat, Oct 31, 2009 at 3:47 PM, manoj singh <mks.amber.gmail.com> wrote:
> The time average properties (energies etc) of the equliberated (relaxed)
> trajectories should be almost same, not the energies some particular
> snapshot.
>
> On Sat, Oct 31, 2009 at 3:39 PM, cyk5056 <cyk5056.163.com> wrote:
>
> > Hi Amberusers,
> >
> > I am doing MD by amber using the following .in file:
> >
> > &cntrl
> > imin=1, maxcyc=1000, ncyc = 500,
> > cut=10.0,
> > ntpr=100, ntx=1, ntb=1, ntr = 1,
> > restraint_wt=5.0,
> > restraintmask=':1-108'
> > &end
> > The output rst files do not match with each other between my own computer
> > and computer cluster of the university. Both of them are running under
> Amber
> > 10 with exactly the same input files. I checked the out file, the
> difference
> > occurs after NSTEP=400.
> > Output file of my own computer:
> > ...
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 300 -3.9166E+04 1.4845E+00 1.6191E+02 CG 386
> > BOND = 2445.9827 ANGLE = 162.1399 DIHED =
> > 994.8353
> > VDWAALS = 4227.8494 EEL = -53419.7262 HBOND =
> > 0.0000
> > 1-4 VDW = 364.8890 1-4 EEL = 5964.5484 RESTRAINT =
> > 93.4892
> > EAMBER = -39259.4815
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 400 -3.9783E+04 1.2726E+00 1.2005E+02 CG 386
> > BOND = 2546.5837 ANGLE = 162.1376 DIHED =
> > 994.4480
> > VDWAALS = 4663.5487 EEL = -54574.8114 HBOND =
> > 0.0000
> > 1-4 VDW = 364.2400 1-4 EEL = 5962.6647 RESTRAINT =
> > 98.2829
> > EAMBER = -39881.1885
> > ...
> > computer cluster:
> > ...
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 300 -3.9166E+04 1.4845E+00 1.6191E+02 CG 386
> > BOND = 2445.9827 ANGLE = 162.1399 DIHED =
> > 994.8353
> > VDWAALS = 4227.8494 EEL = -53419.7262 HBOND =
> > 0.0000
> > 1-4 VDW = 364.8890 1-4 EEL = 5964.5484 RESTRAINT =
> > 93.4892
> > EAMBER = -39259.4815
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 400 -3.9783E+04 1.2727E+00 1.2004E+02 CG 386
> > BOND = 2546.5825 ANGLE = 162.1358 DIHED =
> > 994.4481
> > VDWAALS = 4663.5314 EEL = -54574.7675 HBOND =
> > 0.0000
> > 1-4 VDW = 364.2398 1-4 EEL = 5962.6647 RESTRAINT =
> > 98.2828
> > EAMBER = -39881.1652
> > ...
> >
> > After NSTEP=400, everything of them is different.
> > I searched the archive of Amber, some one says that 32-bit and 64-bit
> > computer will differ. That is partially true for me because cluster is
> using
> > 64-bit and I am using 32-bit. I am trying to let the cluster ran under
> > 32-bit to see if this is the reason. However, they said that is minor
> error.
> > That is not true for me. This step is just a starting point. After
> several
> > simulations based on the results here, the final results are quite
> > different. Which one should I trust? And how to eliminate this problem?
> >
> > Thank you very much!!
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Oct 31 2009 - 13:00:05 PDT
