Re: [gmx-users] Related to energy minimization
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 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 > > > 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 > > > 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 > > >
Re: [gmx-users] Related to energy minimization
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 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 > > 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 > > 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 > > > > 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? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > > or > > > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > > > > > > Gromacs Users mailing list > > > > > > > > > > > > * Please search the archive at > > > > > >
Re: [gmx-users] Related to energy minimization
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 > 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 > 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 > > > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > * For (un)subscribe requests visit > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > > or > > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > > > > Gromacs Users mailing list > > > > > > > > > > * Please search the archive at > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > > posting! > > > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > > -- > > > > Ishrat Jahan > > > > Research Scholar > > > >
Re: [gmx-users] Related to energy minimization
Then I think we need to delete all the waters from protein surface On Tue, Sep 11, 2018 at 10:06 AM, ISHRAT JAHAN 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 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 > > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > * For (un)subscribe requests visit > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > > or > > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > > posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > -- > > > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the
Re: [gmx-users] Related to energy minimization
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 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 > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > -- > > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Workstation choice
d.poly-ch2 from gmxbench-3.0.tar.gz available at: http://www.gromacs.org/About_Gromacs/Benchmarks 6000 atoms timestep 0.001 On 09/10/2018 11:37 PM, Albert wrote: May I ask how many atoms in the system? Which forcefield did you use? And what's the time step? regards On 09/10/2018 09:14 PM, Olga Selyutina wrote: (50 ts instead of 5000 ts, otherwise it's too fast) That would be a factor of about 227! On an available machine (not used for simulations) self-compiled 2018.3, CUDA 9.1 the similar result, factor is about 136: Working dir: /home/user/dev/gromacs/gmxbench-3.0/d.poly-ch2 Command line: gmx mdrun -ntmpi 1 -nt 6 Running on 1 node with total 6 cores, 6 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1050 Ti, compute cap.: 6.1, ECC: no, stat: compatible On 1 MPI rank, each using 6 OpenMP threads Core t (s) Wall t (s) (%) Time: 1102.853 183.809 600.0 (ns/day) (hour/ns) Performance: 235.027 0.102 Finished mdrun on rank 0 Tue Sep 11 01:53:36 2018 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] core-dumped
Dear all, During nvt equilibration I am getting the following error gmx mdrun -v -s npt.tpr -deffnm npt :-) GROMACS - gmx mdrun, 2016.5 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016.5 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/workstation/Documents/GROMACS_projects/GROMACS_GCGR_GLUCAGON_2 Command line: gmx mdrun -v -s npt.tpr -deffnm npt Running on 1 node with total 4 cores, 4 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: AVX2_256 Hardware topology: Basic Reading file npt.tpr, VERSION 2016.5 (single precision) Changing nstlist from 5 to 25, rlist from 1.2 to 1.233 Using 1 MPI thread Using 4 OpenMP threads WARNING: This run will generate roughly 6779 Mb of data starting mdrun '5YQZ_preprocessed - hbond-opt in water' 20 steps,400.0 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 7.344571, max 575.613892 (between atoms 18720 and 18723) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2379 2380 37.50.0872 0.1066 0.1010 2381 2382 47.90.1498 0.1052 0.1090 2383 2384 47.40.0884 0.1147 0.1090 2389 2390 49.10.0597 0.1001 0.0960 2426 2427 90.00.1253 0.1266 0.1080 4036 4037 54.90.1454 0.1077 0.1090 4038 4039 46.10.1081 0.1121 0.1090 4040 4041 30.20.0554 0.1124 0.1090 4040 4042 32.80.1002 0.1123 0.1090 4040 4043 35.10.1426 0.1129 0.1090 5382 5384 50.30.1280 0.1093 0.1090 5956 5957 37.00.0770 0.1141 0.1090 5956 5959 89.80.1805 0.1828 0.1090 5960 5961 61.70.1651 0.1267 0.1229 6029 6031 89.90.1146 1.2008 0.1090 6035 6036 31.60.1083 0.1036 0.1010 6038 6040 42.50.1324 0.1043 0.1010 6887 6888 31.10.1070 0. 0.1090 6887 6889 59.50.1351 0.1100 0.1090 13006 13007 42.30.1575 0.1385 0.1610 13007 13008 41.70.1436 0.1329 0.1480 13007 13009 90.00.1348 0.2201 0.1480 13007 13010 38.20.1530 0.1563 0.1610 18672 18673 86.00.1515 0.2646 0.1530 18673 18674 92.00.1407 1.1474 0.1430 18674 18675 124.60.1445 23.3042 0.1610 18675 18677 82.60.1723 23.9350 0.1480 18675 18678 106.90.1522 23.6614 0.1610 18678 18679 89.60.1402 0.9389 0.1430 18679 18680 92.00.1552 0.1875 0.1530 18723 18724 62.70.1687 73.2199 0.1470 18724 18725 89.50.1607 0.8262 0.1530 18725 18726 90.80.1420 0.1872 0.1430 18720 18723 156.70.1620 84.7622 0.1470 18721 18723 66.70.1602 72.9378 0.1470 18722 18723 67.90.1335 72.8562 0.1470 20543 20544 88.90.1496 0.1505 0.1470 20544 20545 30.80.1570 0.1781 0.1530 20540 20543 89.50.1331 0.2780 0.1470 20541 20543 89.30.1499 0.1735 0.1470 20542 20543 89.20.1426 0.1755 0.1470 Wrote pdb files with previous and current coordinates step 0 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.060079, max 4.753909 (between atoms 18723 and 18724) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous,
Re: [gmx-users] Number of glucose molecules
Please answer my question. Are you a high school student, or do you actually hold an academic degree from an accredited institution? Alex Dear Alex Thank you so much for your kind words. We are not doing "medical research", we are trying to do and understand some basic science only. Are 11 molecules enough to bring about changes in the structure of human serum albumin in simulation; with 41000 water molecules in the simulation box. Can you kindly shed some light on it? Thank You Regards Zaved -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Number of glucose molecules
> Message: 5 > Date: Sun, 9 Sep 2018 02:47:12 -0600 > From: Alex > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Number of glucose molcules > Message-ID: <870d39f7-471b-93f2-2444-6c432717f...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed Dear Alex Thank you so much for your kind words. We are not doing "medical research", we are trying to do and understand some basic science only. Are 11 molecules enough to bring about changes in the structure of human serum albumin in simulation; with 41000 water molecules in the simulation box. Can you kindly shed some light on it? Thank You Regards Zaved > People dear to my heart have diabetes, so... > > If you do not mind my asking, are you a high school student, or are you > actually a graduate student/postdoc? If it is the latter, please do the > humanity favor and send me the name of your advisor, because god forbid > medical research is done by people with gaps in knowledge of this > magnitude. I know I have been criticized on this forum for being less > than polite, but if any of us have a shred of integrity, we must do > something when medical research is concerned. > > If you are a secondary/high school student, the answer is below. > > The concentration is c = rho/mu, where rho is your density of 240mg/dL = > 2.4 g/L and mu = 180.156 g/mol is the molar mass of glucose. This yields > c = 0.0133M and c times the volume of the box is 11 molecules of glucose. > > Alex > > > On 9/9/2018 12:28 AM, za...@tezu.ernet.in wrote: >> Dear Gromacs Users >> >> I have performed a simulation for native protein using gromacs. >> Now I want to add glucose molecules (in order to mimic diabetes >> condition) >> with eg. 240 mg/dL concentration. >> Can anyone help me with the calculation of the number of glucose >> molecules >> I need to add? >> The size of the simulation box is 10.98 * 10.98 * 10.98 nm. >> >> I appreciate any kind response. >> >> Regards >> Zaved * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Fwd: How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?
-- Forwarded message - From: rose rahmani Date: Mon, 10 Sep 2018, 12:58 Subject: How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface? To: Gromacs Hi, How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation? is it possible by GROMACS? gmx gangle? would you please help me? To be clear; i refer you to these plots https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface Best regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Workstation choice
May I ask how many atoms in the system? Which forcefield did you use? And what's the time step? regards On 09/10/2018 09:14 PM, Olga Selyutina wrote: (50 ts instead of 5000 ts, otherwise it's too fast) That would be a factor of about 227! On an available machine (not used for simulations) self-compiled 2018.3, CUDA 9.1 the similar result, factor is about 136: Working dir: /home/user/dev/gromacs/gmxbench-3.0/d.poly-ch2 Command line: gmx mdrun -ntmpi 1 -nt 6 Running on 1 node with total 6 cores, 6 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1050 Ti, compute cap.: 6.1, ECC: no, stat: compatible On 1 MPI rank, each using 6 OpenMP threads Core t (s) Wall t (s)(%) Time: 1102.853183.809 600.0 (ns/day)(hour/ns) Performance: 235.0270.102 Finished mdrun on rank 0 Tue Sep 11 01:53:36 2018 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Workstation choice
On 10.09.2018 21:15, Olga Selyutina wrote: >> >> >> (50 ts instead of 5000 ts, otherwise it's too fast) >> >> >> That would be a factor of about 227! > > > On an available machine (not used for simulations) > self-compiled 2018.3, CUDA 9.1 > the similar result, factor is about 136: > > Working dir: /home/user/dev/gromacs/gmxbench-3.0/d.poly-ch2 > Command line: >gmx mdrun -ntmpi 1 -nt 6 > > Running on 1 node with total 6 cores, 6 logical cores, 1 compatible GPU > Hardware detected: >CPU info: > Vendor: Intel > Brand: Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz > >GPU info: > Number of GPUs detected: 1 > #0: NVIDIA GeForce GTX 1050 Ti, compute cap.: 6.1, ECC: no, stat: > compatible > > On 1 MPI rank, each using 6 OpenMP threads > > Core t (s) Wall t (s)(%) > Time: 1102.853183.809 600.0 > (ns/day)(hour/ns) > Performance: 235.0270.102 > Finished mdrun on rank 0 Tue Sep 11 01:53:36 2018 How would the 8600K perform without GPU (using the "-nb cpu" option on the mdrun binary)? The Ryzen 1700X does the following (-nb cpu): Core t (s) Wall t (s)(%) Time: 4886.335 305.396 1600.0 (ns/day)(hour/ns) Performance: 141.4560.170 Finished mdrun on rank 0 Mon Sep 10 22:21:40 2018 That's still a factor 82 compared to Bratin Kumar's setup. M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Workstation choice
> > > (50 ts instead of 5000 ts, otherwise it's too fast) > > > That would be a factor of about 227! On an available machine (not used for simulations) self-compiled 2018.3, CUDA 9.1 the similar result, factor is about 136: Working dir: /home/user/dev/gromacs/gmxbench-3.0/d.poly-ch2 Command line: gmx mdrun -ntmpi 1 -nt 6 Running on 1 node with total 6 cores, 6 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Core(TM) i5-8600K CPU @ 3.60GHz GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1050 Ti, compute cap.: 6.1, ECC: no, stat: compatible On 1 MPI rank, each using 6 OpenMP threads Core t (s) Wall t (s)(%) Time: 1102.853183.809 600.0 (ns/day)(hour/ns) Performance: 235.0270.102 Finished mdrun on rank 0 Tue Sep 11 01:53:36 2018 -- Best regards, Olga Selyutina -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Workstation choice
On 10.09.2018 20:22, Benson Muite wrote: > Some results (probably suboptimal) for d.poly-ch2 on a desktop running > Fedora 28 and using Gromacs-Opencl from Fedora repositories: > ... > Running on 1 node with total 8 cores, 8 logical cores, 1 compatible GPU > Hardware detected: > CPU info: > Vendor: AMD > Brand: AMD FX(tm)-8350 Eight-Core Processor > GPU info: > Number of GPUs detected: 1 > #0: name: Radeon RX 560 Series (POLARIS11 / DRM 3.23.0 / > > ... > Average per-step force GPU/CPU evaluation time ratio: 2.170 ms/17.768 ms > = 0.122 > > Core t (s) Wall t (s) (%) > Time: 2001.585 250.198 800.0 > (ns/day) (hour/ns) > Performance: 1.727 13.897 > Finished mdrun on rank 0 Mon Sep 10 21:04:37 2018 For your record: self-compiled 2018.3, CUDA 9.2, R-1700X, GTX-1080, (50 ts instead of 5000 ts, otherwise it's too fast) CPU info: Vendor: AMD Brand: AMD Ryzen 7 1700X Eight-Core Processor GPU info: Number of GPUs detected: 1 #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC: no, stat: ... Core t (s) Wall t (s)(%) Time: 1764.209 110.263 1600.0 (ns/day)(hour/ns) Performance: 391.7910.061 Finished mdrun on rank 0 Mon Sep 10 20:42:22 2018 That would be a factor of about 227! M. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Workstation choice
Some results (probably suboptimal) for d.poly-ch2 on a desktop running Fedora 28 and using Gromacs-Opencl from Fedora repositories: Log file opened on Mon Sep 10 21:00:25 2018 Host: mikihir pid: 32669 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2018.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof Aleksei Iupinov Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2017, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2018.2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/benson/Projects/GromacsBench/d.poly-ch2 Command line: gmx mdrun GROMACS version: 2018.2 Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: OpenCL SIMD instructions: SSE2 FFT library: fftw-3.3.5-sse2-avx RDTSCP usage: disabled TNG support: enabled Hwloc support: hwloc-1.11.6 Tracing support: disabled Built on: 2018-07-19 19:45:21 Built by: mockbuild@ [CMAKE] Build OS/arch: Linux 4.17.3-200.fc28.x86_64 x86_64 Build CPU vendor: Intel Build CPU brand: Intel Core Processor (Haswell, no TSX) Build CPU family: 6 Model: 60 Stepping: 1 Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma intel lahf mmx msr pcid pclmuldq popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 8.1.1 C compiler flags: -msse2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 8.1.1 C++ compiler flags: -msse2 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -DNDEBUG -funroll-all-loops -fexcess-precision=fast OpenCL include dir: /usr/include OpenCL library: /usr/lib64/libOpenCL.so OpenCL version: 2.0 Running on 1 node with total 8 cores, 8 logical cores, 1 compatible GPU Hardware detected: CPU info: Vendor: AMD Brand: AMD FX(tm)-8350 Eight-Core Processor Family: 21 Model: 2 Stepping: 0 Features: aes amd apic avx clfsh cmov cx8 cx16 f16c fma fma4 htt lahf misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop Hardware topology: Full, with devices Sockets, cores, and logical processors: Socket 0: [ 0] [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] Numa nodes: Node 0 (16714620928 bytes mem): 0 1 2 3 4 5 6 7 Latency: 0 0 1.00 Caches: L1: 16384 bytes, linesize 64 bytes, assoc. 4, shared 1 ways L2: 2097152 bytes, linesize 64 bytes, assoc. 16, shared 2 ways L3: 8388608 bytes, linesize 64 bytes, assoc. 64, shared 8 ways PCI devices: :01:00.0 Id: 1002:67ef Class: 0x0300 Numa: 0
[gmx-users] Problem while equilibrating system with frozen groups
Hi, I am simulating DNA (infinite) protein Martini system with electric field. I have 2 systems, for 1 complete DNA is frozen and for the 2nd one, only 4 atoms of the DNA is frozen. When I perform NPT equilibration for the complete DNA frozen system, it shows me this error : Fatal error: 4442 particles communicated to PME rank 24 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. But it runs fine for the other system with 4 DNA atoms frozen. For the completely frozen DNA, if I freeze only 2 dimensions, letting 1 dimension free it runs without complaining. I do not understand why it shows problem for the completely frozen DNA with 3 dimensions frozen? Since the DNA is infinite I use semi-isotropic pressure coupling keeping the compressibility along Z 0. So the pressure coupling options in my .mdp file looks like this : freezegrps = DNA freezedim = Y N Y ; Pressure coupling is off ;pcoupl = no; no pressure coupling in NVT Pcoupl = parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 3e-4 0 ref_p = 1.0 1.0 refcoord_scaling = all I tried it for finite DNA too and it shows same problem for completely frozen DNA. I ran the completely Frozen DNA system keeping 1 dimension free, and freezing the other 2 dimensions. I ran the equilibration run for 500 ps. I plotted the pressure and the average pressure is 9.15 bar, while the target pressure that I had put in the .mdp file is 1 bar. So there is a large difference. I was searching regarding this problem, and I found that I need to use "energygrp-excl" for frozen groups. So I ran the completely frozen DNA system with energygrp-excl = DNA, using cutoff-scheme = group (since energygrp-excl is not supported in Verlet in my gromacs version 5.0.6), and the average pressure I get is again 9.28 bar. For the system with 4 DNA atoms frozen, the average pressure shows 5.17 bar, which is still different from the target pressure. I am now running these equilibration runs for longer (4 ns), to see if that helps to get the average pressure closer to 1 bar. Normally when all atoms are free what I found was 0.5 ns was enough to get average pressure 1 bar, and equilibrate the system. But I don't understand what is the problem I am facing here with frozen atoms? I turn off the electric field during the equilibration runs. I would highly appreciate any help! Thank you very much, Regards, Arnab -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
On 9/10/18 9:14 AM, Bratin Kumar Das wrote: Use -maxwarn 2 at the last of your gmx grompp ... command No! One should *never* use -maxwarn just to circumvent problems. It is clear that there is some modification to ffnonbonded.itp that is syntactically incorrect. grompp will not have the right parameters and any process that tries to use this .tpr file will fail. -Justin On Mon, Sep 10, 2018, 6:19 PM saranya wrote: Dear Users, My simulation system is Amyloid β Protein (1-42) with Fe2+ complex and i am using OPLSAA forcefield for the simulations. I edited the ffbonded.itp files accordingly as mentioned in the tutorials. While running grompp command, I get following error: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, VERSION 5.1.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Setting the LD random seed to 2295799000 WARNING 1 [file ffnonbonded.itp, line 3]: Too few parameters on line (source file /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line 283) Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file c5.top, line 5912]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are:42Protein residues There are: 1 Other residues There are: 8015 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 49971.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx grompp, VERSION 5.1.2 Source code file: /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 2107 Fatal error: Too many warnings (1), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Anyone can help me in overcoming this fatal error will be appreciated. With Regards, Saranya Vasudevan, Research Scholar, Molecular Quantum Mechanics Laboratory, Department of Physics, Bharathiar University, Coimbatore-46 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. --
Re: [gmx-users] (no subject)
Use -maxwarn 2 at the last of your gmx grompp ... command On Mon, Sep 10, 2018, 6:19 PM saranya wrote: > Dear Users, > > My simulation system is Amyloid β Protein (1-42) with Fe2+ complex > and i am using OPLSAA forcefield for the simulations. I edited the > ffbonded.itp files accordingly as mentioned in the tutorials. > > While running grompp command, I get following error: > > > > gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr > > :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: > > > > GROMACS is written by: > > Emile Apol Rossen Apostolov Herman J.C. BerendsenPar > Bjelkmar > > Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch > > Gerrit Groenhof Christoph Junghans Anca HamuraruVincent > Hindriksen > > Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner > > Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff > >Erik Marklund Teemu Murtola Szilard Pall Sander Pronk > >Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers > >Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf > >and the project leaders: > > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel > > > > Copyright (c) 1991-2000, University of Groningen, The Netherlands. > > Copyright (c) 2001-2015, The GROMACS development team at > > Uppsala University, Stockholm University and > > the Royal Institute of Technology, Sweden. > > check out http://www.gromacs.org for more information. > > > > GROMACS is free software; you can redistribute it and/or modify it > > under the terms of the GNU Lesser General Public License > > as published by the Free Software Foundation; either version 2.1 > > of the License, or (at your option) any later version. > > > > GROMACS: gmx grompp, VERSION 5.1.2 > > Executable: /usr/local/gromacs/bin/gmx > > Data prefix: /usr/local/gromacs > > Command line: > > gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr > > > > Ignoring obsolete mdp entry 'title' > > > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# > > Setting the LD random seed to 2295799000 > > > > WARNING 1 [file ffnonbonded.itp, line 3]: > > Too few parameters on line (source file > > /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, > > line 283) > > > > Generated 335790 of the 335790 non-bonded parameter combinations > > Generating 1-4 interactions: fudge = 0.5 > > Generated 335790 of the 335790 1-4 parameter combinations > > Excluding 3 bonded neighbours molecule type 'Protein_chain_A' > > Excluding 2 bonded neighbours molecule type 'SOL' > > > > NOTE 1 [file c5.top, line 5912]: > > System has non-zero total charge: -2.00 > > Total charge should normally be an integer. See > > http://www.gromacs.org/Documentation/Floating_Point_Arithmetic > > for discussion on how close it should be to an integer. > > > > > > > > Removing all charge groups because cutoff-scheme=Verlet > > Analysing residue names: > > There are:42Protein residues > > There are: 1 Other residues > > There are: 8015 Water residues > > Analysing Protein... > > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > into groups... > > Number of degrees of freedom in T-Coupling group rest is 49971.00 > > Calculating fourier grid dimensions for X Y Z > > Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113 > > Estimate for the relative computational load of the PME mesh part: 0.23 > > This run will generate roughly 2 Mb of data > > > > There was 1 note > > > > There was 1 warning > > > > --- > > Program gmx grompp, VERSION 5.1.2 > > Source code file: > /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, > line: 2107 > > > > Fatal error: > > Too many warnings (1), gmx terminated. > > If you are sure all warnings are harmless, use the -maxwarn option. > > For more information and tips for troubleshooting, please check the GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > Anyone can help me in overcoming this fatal error will be appreciated. > > > > > > With Regards, > > Saranya Vasudevan, > > Research Scholar, > > Molecular Quantum Mechanics Laboratory, > > Department of Physics, > > Bharathiar University, > > Coimbatore-46 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Related to energy minimization
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 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 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > 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? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] (no subject)
Dear Users, My simulation system is Amyloid β Protein (1-42) with Fe2+ complex and i am using OPLSAA forcefield for the simulations. I edited the ffbonded.itp files accordingly as mentioned in the tutorials. While running grompp command, I get following error: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr :-) GROMACS - gmx grompp, VERSION 5.1.2 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch Gerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios KarkoulisPeter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter TielemanTeemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx grompp, VERSION 5.1.2 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx grompp -f em.mdp -c solv.gro -p c5.top -o ions.tpr Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Setting the LD random seed to 2295799000 WARNING 1 [file ffnonbonded.itp, line 3]: Too few parameters on line (source file /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/toppush.c, line 283) Generated 335790 of the 335790 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 335790 of the 335790 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file c5.top, line 5912]: System has non-zero total charge: -2.00 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Removing all charge groups because cutoff-scheme=Verlet Analysing residue names: There are:42Protein residues There are: 1 Other residues There are: 8015 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 49971.00 Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x56x56, spacing 0.113 0.113 0.113 Estimate for the relative computational load of the PME mesh part: 0.23 This run will generate roughly 2 Mb of data There was 1 note There was 1 warning --- Program gmx grompp, VERSION 5.1.2 Source code file: /home/mqml/Downloads/gromacs-5.1.2/src/gromacs/gmxpreprocess/grompp.c, line: 2107 Fatal error: Too many warnings (1), gmx terminated. If you are sure all warnings are harmless, use the -maxwarn option. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Anyone can help me in overcoming this fatal error will be appreciated. With Regards, Saranya Vasudevan, Research Scholar, Molecular Quantum Mechanics Laboratory, Department of Physics, Bharathiar University, Coimbatore-46 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Related to energy minimization
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 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? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- 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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Related to energy minimization
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 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? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Related to energy minimization
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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How can i calculate the (ADF)angular distribution of the angles between water molecule water and surface?
Hi, How can i calculate the angular distribution of the angles between water molecule water and surface? surface during molecular dynamics simulation? is it possible by GROMACS? gmx gangle? would you please help me? To be clear; i refer you to these plots https://www.researchgate.net/post/How_can_i_calculate_the_ADFangular_distribution_of_the_angles_between_water_molecule_water_and_surface Best regards Rose -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Segmentation fault (core dumped)
Please pest the entire error lines in this mailing list. It may possible due to lack of proper minimization of your starting coordinates. On Mon, Sep 10, 2018, 11:22 AM Ashma khan wrote: > When I am running the gmx mdrun -v -deffnm 5e61_nvt there is an error of > core dumped.I have increased the equilibration time but the same error has > occured.So,please suggest me what should I do > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] electric field amplitude of a photon
Hi all, Gromacs manual section 6.7 refers to this paper: https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.200703987 so I guess my question is for David. What is unclear is how the electric field amplitudes were estimated (text below Eq. 1). I mean, we can of course get something like sqrt[ I/(eps_0 x c)] (it also seems there might be a typo in the left column of p. 1417 of the paper -- there should not be 1/2, if one includes the energy of the magnetic field to actually equate the E_0-based value to the total intensity). That possible typo aside, is that where the values of E_0 came from? Granted, all of this is very approximate, trying to mimic quantum physics with a painfully classical picture, but for consistency and so I could properly cite this work if needed, it might be useful to know how these values were calculated. My case is non-pulsed, but that's irrelevant. Thanks! Alex -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
