[gmx-users] Very high energies after energy minimization

[Deep Bhattacharya]

Hello Evan,

I am using the SPC solvent model.
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

Posre.itp from pdb2gmx for the protein
; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1  1000  1000  1000
     5     1  1000  1000  1000
     6     1  1000  1000  1000
     7     1  1000  1000  1000
     8     1  1000  1000  1000
     9     1  1000  1000  1000
    10     1  1000  1000  1000
Cut out the initial part, remains constant throughout the same.

Please suggest what changes can I do.

Sincerely,
Deep Bhattacharya

On Wed, Jul 27, 2016 at 2:35 PM, Evan Lowry <evanwlowry at gmail.com> wrote:

> 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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-- 
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616