[AMBER] : Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations?

From: Li Dailin <lidl25.hotmail.com>
Date: Sat, 13 Mar 2021 00:26:57 +0000

Hi Adrian,

Thanks for your reply. Is there any other method to do the job (pull only a ion along the pathway)?

Best,

Dailin

-----ʼԭ-----
: Adrian Roitberg [mailto:roitberg.ufl.edu]
ʱ: 2021313 04:21
ռ: amber.ambermd.org
: Re: [AMBER] Why a target ion failed to move along the pathway in the simulated annealing version of Nudged Elastic Band (NEB) calculations?

I am not sure, but thinking about the code and what it does, I do not think it could ever work with just ONE particle in the NEB mask.

Adrian


On 3/11/21 8:55 PM, Li Dailin wrote:
> [External Email]
>
> 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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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry Department of Chemistry University of Florida roitberg.ufl.edu
352-392-6972


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Received on Fri Mar 12 2021 - 16:30:02 PST
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