[AMBER] Energy bumps and structure deformation while minimization of a small molecule

From: Kotaro TANAKA via AMBER <amber.ambermd.org>
Date: Wed, 28 Jun 2023 14:16:41 +0900

Hi,

I performed a 1000 step energy minimization of a small organic molecule,
which is prepared by antechamber with GAFF2 and the RESP-derived charges.

While the final configuration after minimization looks fine, but there
were occasional huge bumps in the potential energy in the course of the
minimization (I attached the energy plot file and the mdout file).

I looked the trajectory and confirmed that the configurations were also
distorted at the timing of the energy bumps.

Has anyone observed any situation like this? What may be the cause of
this behavior?

# software version: Amber22/AmberTools22

# Example of the energy bump (line 3952-3997 of the attached min.out
file. The corresponding trajectory snapshots are also attached.) :
    NSTEP       ENERGY RMS            GMAX         NAME    NUMBER
     479       4.2420E+01     5.0983E-02     1.3987E-01 C11        15

  BOND    =        1.7474  ANGLE   =       14.0204  DIHED = 9.6009
  VDWAALS =       -3.2458  EEL     =      -60.2337  HBOND = 0.0000
  1-4 VDW =        6.5164  1-4 EEL =       74.0143  RESTRAINT =       
0.0000


    NSTEP       ENERGY          RMS            GMAX NAME    NUMBER
     480       1.4703E+04     1.5718E+04     6.7010E+04 C11        15

  BOND    =     1990.7664  ANGLE   =      737.5050  DIHED = 53.9941
  VDWAALS =       -0.8177  EEL     =      -62.7268  HBOND = 0.0000
  1-4 VDW =    11889.5108  1-4 EEL =       95.2040  RESTRAINT =       
0.0000


    NSTEP       ENERGY          RMS            GMAX NAME    NUMBER
     481       9.9038E+02     2.5920E+02     9.5956E+02 C11        15

  BOND    =      561.1639  ANGLE   =      338.1107  DIHED = 21.0169
  VDWAALS =       -2.3347  EEL     =      -61.6524  HBOND = 0.0000
  1-4 VDW =       53.2071  1-4 EEL =       80.8659  RESTRAINT =       
0.0000


    NSTEP       ENERGY          RMS            GMAX NAME    NUMBER
     482       4.2420E+01     3.8712E-02     1.1602E-01 O1         11

  BOND    =        1.7456  ANGLE   =       14.0208  DIHED = 9.6006
  VDWAALS =       -3.2456  EEL     =      -60.2342  HBOND = 0.0000
  1-4 VDW =        6.5169  1-4 EEL =       74.0157  RESTRAINT =       
0.0000

Best Regards,
Kotaro




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Received on Tue Jun 27 2023 - 22:30:03 PDT