[gmx-users] Related to energy minimization

[Bratin Kumar Das]

You upload the warning given by mdrun. I think there is a problem with the
initial configuration of your .pdb file. Please upload all the lines
written in your terminal during mdrun operation

On Mon, Sep 10, 2018, 4:13 PM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:

> 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
> > > --
> > > Gromacs Users mailing list
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>
> --
> Ishrat Jahan
> Research Scholar
> Department Of Chemistry
> A.M.U Aligarh
> --
> Gromacs Users mailing list
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