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!!
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Received on Sat Oct 31 2009 - 13:00:03 PDT
