Dear All,
Now I'm learning Amber8 by performing Workshop Tutorial 1(
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/index.htm) step by step, but when I perform minimization before MD, I got different results compared with theirs. I examined the two out files carefully and find that: the results of steepest descent minimizations are completely same, but after 50 conjugate gradient minimizations the results begin to be different bit by bit, the final results are :
My result:
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -3.9091E+04 7.9419E-01 3.5390E+01 Na+ 641
BOND = 2859.5296 ANGLE = 435.5573 DIHED = 452.7539
VDWAALS = 6985.1288 EEL = -50065.8360 HBOND = 0.0000
1-4 VDW = 248.0616 1-4 EEL = -294.5216 RESTRAINT = 288.7350
Their result:
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -3.8989E+04 5.9208E-01 2.7355E+01 P 446
BOND = 2829.9826 ANGLE = 433.7389 DIHED = 452.8278
VDWAALS = 6893.6489 EEL = -49839.8168 HBOND = 0.0000
1-4 VDW = 248.3104 1-4 EEL = -294.6786 RESTRAINT = 286.5245
EAMBER = -39275.9867
Now my question is : Are these differences in conjugate gradient minimization in error range? Did these differences come from so-called "different machines" in manual Page 10?
Any advice will be greatly appreciated!
sincerely yours,Zhihong Yu
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Received on Wed May 03 2006 - 06:07:05 PDT
