Hi,
I intend to pull a K+ ion to move along an ion channel (more than 1000 amino residues) in the simulated annealing version of NEB simulations (Amber18), based on the Amber Tutorial 6.6. The jobs could finish normally, however, the target K+ ion did not move and just stayed as in the double end points (initial and final structures) throughout the simulation stages (heating, equilibrating, simulated annealing, ...), no matter how large the pulling force is (skmin/skmax = 10 ~ 5000). The input and output files of the equilibration stage are listed below.
Input file (equilibration stage):
&cntrl
Imin = 0, irest = 1, ntx = 5, igb = 1, ntb = 0, cut = 999, ntc = 2, ntf = 2,
Ntt = 3, gamma_ln = 1000.0, saltcon = 0.2,
Nstlim = 500000, dt = 0.002, ioutfm = 1, ntxo = 2,
Ntpr = 5000, ntwx = 50000, ntwr = 50000, ig = -1,
temp0 = 300.0,
tgtfitmask = ":1318",
tgtrmsmask = ":1318", (# The residue 1318 is the target K+ ion)
ineb = 1, skmin = 5000, skmax = 5000,
/
Output file (the last step and averages):
NSTEP = 500000 TIME(PS) = 1200.000 TEMP(K) = 303.52 PRESS = 0.0
Etot = -19202.5394 EKtot = 16391.3086 EPtot = -35593.8480
BOND = 4266.3934 ANGLE = 10950.4327 DIHED = 17323.5818
1-4 NB = 4964.0690 1-4 EEL = 53531.0571 VDWAALS = -11263.2521
EELEC= -95209.5891 EGB = -20156.5407 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -51475.5670
Energy for replicate 2 = -35441.3415
Energy for replicate 3 = -35478.5552
Energy for replicate 4 = -35444.8940
Energy for replicate 5 = -35541.9040
Energy for replicate 6 = -35304.6905
Energy for replicate 7 = -35430.2560
Energy for replicate 8 = -35298.4472
Energy for replicate 9 = -35593.8480
Energy for replicate 10 = -51365.6858
Total Energy of replicates = -386375.1892
------------------------------------------------------------------------------
A V E R A G E S O V E R 100 S T E P S
NSTEP = 500000 TIME(PS) = 1200.000 TEMP(K) = 299.83 PRESS = 0.0
Etot = -19241.8113 EKtot = 16192.1339 EPtot = -35433.9452
BOND = 4292.8217 ANGLE = 11070.3246 DIHED = 17397.3694
1-4 NB = 4924.4078 1-4 EEL = 53580.2989 VDWAALS = -11299.9451
EELEC = -95522.7562 EGB = -19876.4662 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -51475.5670
Energy for replicate 2 = -35441.3415
Energy for replicate 3 = -35478.5552
Energy for replicate 4 = -35444.8940
Energy for replicate 5 = -35541.9040
Energy for replicate 6 = -35304.6905
Energy for replicate 7 = -35430.2560
Energy for replicate 8 = -35298.4472
Energy for replicate 9 = -35593.8480
Energy for replicate 10 = -51365.6858
Total Energy of replicates = -386375.1892
Questions:
(1) What is wrong with the input file? How to pull the target K+ ion along the pathway?
(2) The energy in the output file does not look fine. The energies of replicate 1 (initial structure) and 10 (final structure) are quite different from the other replicas, which is not the same way as the Amber Tutorial 6.6. I have double checked the structures from each replica and found replicate 1-5 get a similar configuration to the initial structure and 6-10 get a similar to the final. Does the energy indicate any problems?
Thank a lot for your help. Looking forward to your reply.
Best,
Dailin
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Received on Thu Mar 11 2021 - 18:00:02 PST
