[gmx-users] Very high energies after energy minimization

[Evan Lowry]

Something is seriously wrong with the system. Do you have a solvent? If so,
use a trajectory viewer to ensure that there aren't solvent molecules on
top of your protein for some reason. Otherwise, it is probably related to
the protein structure clashing with itself (e.g., atoms are too close or
charges are incorrect). Additionally, what is in your positional restraint
file? Maybe you are arbitrarily restraining things that shouldn't be
restrained. Those are some things to check.

Evan L.

On Wed, Jul 27, 2016 at 1:04 PM, Deep Bhattacharya <hypergenetics at gmail.com>
wrote:

> 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
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