Dear AMBER users,
I'm trying to perform NEB for a system composed by 304 residues in explicit solvent. The QM part of this system in which some of the residues are involved in an enzymatic reaction is treated at PM6 level. The starting and ending point structures were previously relaxed and minimized appropriately for the NEB so that the Potential energy gap between them is around 24 Kcal/mol. This value is near to that expected for this kind of reaction.
Even so, I don't understand why the potential energy of the others copies dramatically goes up just after the beginning of the first heating step. As can see by the following output, the energy difference between the copies and the fixed points is around 10.000 kcal/mol.
I tried to run changing some input parameters like spring constant and Langevin frequency, but I had the same results.
Here following the input I've used, and the outcomes obtained.
Best Regards,
Simone
neb
&cntrl
imin=0,
irest=0,
cut=8.0,
ntpr=100, ntwr=100, ntwx=100, ioutfm=1,
ntf=2, ntc=2,
ntt=3, gamma_ln=1000.0, ig=-1,
nstlim=40000, dt=0.0005,
tempi=0.0, temp0=300.0,
ntb=1, ntp=0,
noshakemask = ':36,231,304,310'
tgtfitmask=":36,231,304,310",
tgtrmsmask=":36,231,304,310",
ineb = 1,skmin = 10,skmax = 10,
ifqnt=1,
nmropt=1,
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
&qmmm
qmmask=':35,36,167,188,190,231,302-304,310,313,316-318',
qmcharge=-4,
qm_theory='PM6',
qmshake=0,
qmcut=8.0,
/
NSTEP = 100 TIME(PS) = 0.050 TEMP(K) = 0.88 PRESS = 0.0
Etot = -102335.0227 EKtot = 49.6085 EPtot = -102384.6313
BOND = 2376.1917 ANGLE = 636.2826 DIHED = 3152.2142
1-4 NB = 917.3374 1-4 EEL = 9380.4532 VDWAALS = 15698.3931
EELEC = -131659.4617 EHBOND = 0.0000 RESTRAINT = 0.0000
PM6ESCF= -2886.0417
NEB replicate breakdown:
Energy for replicate 1 = -112138.5260
Energy for replicate 2 = -102384.9305
Energy for replicate 3 = -102384.6313
Energy for replicate 4 = -102384.5845
Energy for replicate 5 = -102384.2176
Energy for replicate 6 = -102384.2919
Energy for replicate 7 = -102384.9233
Energy for replicate 8 = -102384.6932
Energy for replicate 9 = -102384.6863
Energy for replicate 10 = -102384.7983
Energy for replicate 11 = -102384.2414
Energy for replicate 12 = -102384.1638
Energy for replicate 13 = -102384.5048
Energy for replicate 14 = -102383.9617
Energy for replicate 15 = -102375.6665
Energy for replicate 16 = -102335.8659
Energy for replicate 17 = -102312.0666
Energy for replicate 18 = -102358.5182
Energy for replicate 19 = -102366.2849
Energy for replicate 20 = -102367.5166
Energy for replicate 21 = -102367.8928
Energy for replicate 22 = -102367.1021
Energy for replicate 23 = -102367.6742
Energy for replicate 24 = -102367.9548
Energy for replicate 25 = -102367.6490
Energy for replicate 26 = -102367.6276
Energy for replicate 27 = -102367.8002
Energy for replicate 28 = -102367.4804
Energy for replicate 29 = -102367.3654
Energy for replicate 30 = -102367.8843
Energy for replicate 31 = -102367.1492
Energy for replicate 32 = -112114.1602
Total Energy of replicates = -3295410.8136
Ewald error estimate: 0.1112E-01
------------------------------------------------------------------------------
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
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Received on Thu Aug 04 2022 - 13:33:04 PDT
