[gmx-users] Related to energy minimization
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Tue Sep 11 09:56:03 CEST 2018
Ya
On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN <jishrat17 at gmail.com> wrote:
> Did your problem of core dumped was solved?
>
> On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das <
> 177cy500.bratin at nitk.edu.in>
> wrote:
>
> > No problem...I did for other proteins also...during NVT ensemble it's
> > concentration will be fixed.
> >
> > On Tue, Sep 11, 2018 at 11:22 AM, ISHRAT JAHAN <jishrat17 at gmail.com>
> > wrote:
> >
> > > 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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