[gmx-users] Related to energy minimization

ISHRAT JAHAN jishrat17 at gmail.com
Tue Sep 11 07:53:15 CEST 2018 

But if i remove the water molecule from protein surface its concentration
will change

On Tue, Sep 11, 2018, 11:10 AM Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
wrote:

> What ever solvent u r using can make badcontact with protein..that's why I
> am suggesting
>
> On Tue, Sep 11, 2018, 10:29 AM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
>
> > Why should we delete all the water from protein surface. Actually i am
> > doing this in simulation in a urea box. How do i remove water from
> protein
> > surface?
> >
> > On Tue, Sep 11, 2018, 10:19 AM Bratin Kumar Das <
> > 177cy500.bratin at nitk.edu.in>
> > wrote:
> >
> > > Then I think we need to delete all the waters from protein surface
> > >
> > > On Tue, Sep 11, 2018 at 10:06 AM, ISHRAT JAHAN <jishrat17 at gmail.com>
> > > wrote:
> > >
> > > > I am getting the same error as u have posted today. Segmentation
> fault
> > > core
> > > > dumped. Although my minimization runs properly.
> > > >
> > > > On Mon, Sep 10, 2018, 6:30 PM Bratin Kumar Das <
> > > > 177cy500.bratin at nitk.edu.in>
> > > > wrote:
> > > >
> > > > > 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
> > > > > > > > --
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> > > > > > Ishrat Jahan
> > > > > > Research Scholar
> > > > > > Department Of Chemistry
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