[gmx-users] Very high energies after energy minimization

[Deep Bhattacharya]

Hello,

I am attempting in performing energy minimization on protein-carbohydrate
complex and I have obtained
*Energy minimization has stopped, but the forces have not converged to the*
*requested precision Fmax < 1000 (which may not be possible for your
system).*
*It stopped because the algorithm tried to make a new step whose size was
too*
*small, or there was no change in the energy since last step. Either way,
we*
*regard the minimization as converged to within the available machine*
*precision, given your starting configuration and EM parameters.*
*You might need to increase your constraint accuracy, or turn*
*off constraints altogether (set constraints = none in mdp file)*

*Steepest Descents converged to machine precision in 193 steps,*
*but did not reach the requested Fmax < 1000.*
*Potential Energy  = -2.25884936387141e+13*
*Maximum force     =  3.70136760562579e+25 on atom 1553*
*Norm of force     =  2.39587460988866e+23*


; minim.mdp - used as input into grompp to generate em.tpr
*define       =  -DPOSRES -DPOSRES_LIGAND*
*integrator = steep *
*emtol = 1000.0   *
*emstep      = 0.001      *
*nsteps = 50000   *
*energygrps              = System*
*nstlist    = 1*
*constraints = none*
*; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions*
*    ; Frequency to update the neighbor list and long range forces*
*ns_type = grid ; Method to determine neighbor list (simple, grid)*
*rlist = 1.0 ; Cut-off for making neighbor list (short range forces)*
*coulombtype = PME ; Treatment of long range electrostatic interactions*
*rcoulomb = 1.0 ; long range electrostatic cut-off*
*rvdw = 1.0 ; long range Van der Waals cut-off*
*pbc         = xyz ;Periodic Boundary Conditions (yes/no)*
*em.mdp*

The maximum force seems unrealistic, how can I solve this issue?
I have substituted charges of my ligand using atomicchargecalculator (DOI:
10.1186/s13321-015-0099-x-- ) in the original file from PRODRG server.
After reading many posts I can infer that there might be come problem in
the topology of the ligand or the protein but I am not to recognize the
actual source of the problem because if I go ahead with  NPT and NVT
equilibration my system is just exploding.

Please help.
Thanks in advance.
*Deep S Bhattacharya*
*Graduate Research Assistant*
Mohs Biomedical Imaging & Nanotechnology Group
Pharmaceutical Sciences
*University of Nebraska Medical Center*
4018 Eppley Science Hall  |  Omaha, NE 68198-6805
office 402.559.4349  | cell 402.906.1640
deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com