Thank u for your instant reply. What changes you have done in mdp file to remove core dump error?
On Tue, Sep 11, 2018, 1:26 PM Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Ya > > On Tue, Sep 11, 2018, 12:45 PM ISHRAT JAHAN <jishra...@gmail.com> wrote: > > > Did your problem of core dumped was solved? > > > > On Tue, Sep 11, 2018, 12:23 PM Bratin Kumar Das < > > 177cy500.bra...@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 <jishra...@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.bra...@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 <jishra...@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.bra...@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 < > > > jishra...@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.bra...@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 < > > > jishra...@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.bra...@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 < > > > > > jishra...@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 > > > > > > > > > > > > > > > > > > > > > > > > * Please search the archive at > > > > > > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX- > > > > Users_List > > > > > > > before > > > > > > > > > > > > posting! > > > > > > > > > > > > > > > > > > > > > > > > * Can't post? 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