[gmx-users] Related to energy minimization
ISHRAT JAHAN
jishrat17 at gmail.com
Tue Sep 11 06:58:50 CEST 2018
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
> > > > A.M.U Aligarh
> > > > --
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