Breaking of the molecular structure after energy minimization

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1

GROMACS version:
GROMACS modification: Yes/No
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I performed energy minimization using the following em.mdp file.

; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.001 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions

As a result of running energy minimization with the file above, the molecular structure of cholesterol was broken, as shown in the image below.

em 전
em 전863×754 203 KB

em 후
em 후858×755 181 KB

I would like to know why this happened and how to solve the problem.

2

No bonds break during MD simulations (or corresponding energy minimization). The bonds shown in pymol are guessed based on distances between atoms. I’m not sure if you can change that threshold distance in pymol.

So, there is nothing wrong with the EM output (related to the bonds). It’s the visual representation that is the problem.

3

See Covalent bond breaks after energy minimization for more details.

4

Thank you for your reply!! :)