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
>
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Received on Sat Oct 31 2009 - 13:00:04 PDT
