[gmx-users] Related to energy minimization

[ISHRAT JAHAN]

Thank u for your reply sir. I have changed the -Dflexible to -DPosres but
still gets the same problem.

On Mon, Sep 10, 2018 at 3:24 PM Bratin Kumar Das <
177cy500.bratin at nitk.edu.in> wrote:

> 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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-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh