Hi Amber users,
I am performing nudged elastic band calculations on a protein system
in explicit solvent. I noticed that the energies for the endpoints
(shown below) are very far from the intermediate points at the end of
my NEB run. I am using the same NEB parameters and protocol as the
Amber tutorial A5, except for those relating to implicit solvent, and
I am running the annealing step for slightly longer since my system is
much bigger than the dipeptide in the tutorial.
NSTEP = 100000 TIME(PS) = 920.000 TEMP(K) = 303.04 PRESS = 86.0
Etot = -84034.0220 EKtot = 21396.2990 EPtot = -105430.3210
BOND = 973.8880 ANGLE = 2603.0690 DIHED = 3338.0910
1-4 NB = 1121.9381 1-4 EEL = 9656.5119 VDWAALS = 11144.1954
EELEC = -134268.0144 EHBOND = 0.0000 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -149601.5096
Energy for replicate 2 = -105224.9213
Energy for replicate 3 = -105284.7919
Energy for replicate 4 = -105322.5168
Energy for replicate 5 = -105368.0022
Energy for replicate 6 = -105706.5105
Energy for replicate 7 = -105285.5549
Energy for replicate 8 = -105215.8000
Energy for replicate 9 = -105175.5311
Energy for replicate 10 = -105407.6115
Energy for replicate 11 = -105404.0531
Energy for replicate 12 = -105189.3027
Energy for replicate 13 = -105329.3757
Energy for replicate 14 = -105476.4810
Energy for replicate 15 = -105281.1999
Energy for replicate 16 = -105475.2188
Energy for replicate 17 = -105476.2020
Energy for replicate 18 = -105321.5064
Energy for replicate 19 = -105077.3354
Energy for replicate 20 = -105388.9111
Energy for replicate 21 = -105456.9010
Energy for replicate 22 = -105234.7272
Energy for replicate 23 = -105358.6921
Energy for replicate 24 = -105423.5303
Energy for replicate 25 = -105446.2198
Energy for replicate 26 = -105189.0672
Energy for replicate 27 = -105585.0960
Energy for replicate 28 = -105197.3642
Energy for replicate 29 = -105354.3470
Energy for replicate 30 = -105188.3794
Energy for replicate 31 = -105430.3210
Energy for replicate 32 = -149554.4709
Total Energy of replicates = -3459431.4522
EKCMT = 8802.7356 VIRIAL = 8169.0047 VOLUME = 341491.8761
Density = 1.0291
Ewald error estimate: 0.7207E-04
Has anyone encountered this "problem" when using explicit solvent for
NEB calculations? Or is this normal for explicit solvent systems? I
have started a trial run using implicit solvent with the same protocol
and the distribution of the energies among the replicates look
reasonable. Would gladly appreciate some help with this. Thanks.
-Yaw Sing
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Received on Thu Nov 08 2012 - 03:00:03 PST
