[gmx-users] Related to energy minimization

[Bratin Kumar Das]

I think you should remove define=-DFLEXIBLE
and define=-DPOSRES in the .mdp file. Give 1000 force constant. Don't
give  large force costant.

On Mon, Sep 10, 2018, 3:14 PM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> Dear all,
> I am trying to do energy minimization of two docked protein. At the energy
> minimization step during MD simulation process, the em.gro file is found to
> be broken due to which equilibration of protein does not occur and core
> dumped error has been found.
> Please help me in this regard. I am attaching my em.mdp file and snapshot
> of em.gro file.
> ; Lines starting with ';' ARE COMMENTS
> ; Everything following ';' is also comment
>
> title           = Energy Minimization   ; Title of run
>
> ; The following line tell the program the standard locations where to find
> certain files
> cpp             = /lib/cpp      ; Preprocessor
>
> ; Define can be used to control processes
> define          = -DFLEXIBLE
>
> ; 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 < 1.0 kJ/mol
> nsteps          = 2000          ; Maximum number of (minimization) steps to
> perform
> nstenergy       = 1             ; Write energies to disk every nstenergy
> steps
> energygrps      = system        ; Which energy group(s) to write to disk
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> ns_type         = grid  ; Method to determine neighbor list (simple, grid)
> coulombtype = PME               ; Longrange electrostatics (Ewald)
> rvdw = 1.0
> rlist = 1.0
> rcoulomb = 1.0
> fourierspacing = 0.12
> pme_order = 4
> ewald_rtol = 1e-5
> constraints     = none          ; Bond types to replace by constraints
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
> [image: Screenshot_from_2018-09-10_14_59_11.jpg]
>
> --
> Ishrat Jahan
> Research Scholar
> Department Of Chemistry
> A.M.U Aligarh
> --
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