Re: [gmx-users] Bond breakage modelling
Thank you Peter, I will try to have a detailed look. Regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Peter Kroon Sent: dinsdag 19 februari 2019 13:41 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Bond breakage modelling I've never done it myself, so not really. The manual should help :) I don't know if Morse potentials come built-in, or that you'll need to make tables. Be aware that if you have three or more morse potential particles together they can and will form stable triangles, because there is no influence of the angle on the potential. Peter On 19-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how to implement it? > Best regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle dependence >> on the potential energy, since the non-bonded potentials must be pair-wise. >> Depending on the exact problem this may be acceptable though. The >> angle dependence on the potential energy also immediately points out >> an issue with your cut-off based approach: how will you deal with the angle(s)? >> >> In literature I have seen some papers of people pulling proteins >> apart, breaking cystein bridges. Those may contain some insight/ideas. >> >> >> Peter >> >>> On 19-02-19 11:28, Ali Khodayari wrote: >>> Dear All, >>> >>> >>> >>> We have simulated a cellulose fiber using GLYCAM06 ff parameters >>> converted to GROMACS. The model is validated and works properly. >>> >>> We are investigating the behavior of the material under tensile load. >>> However, as covalent bonds are modelled with a harmonic potential >>> -as it is in most of the non-reactive force fields- some parameters >>> cannot be extracted. Is there any way to mimic the breakage of the >>> bonds, let's say when the distance of the atoms exceed a certain >>> amount? In other words, if we have a rough idea of the strain at >>> which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? >>> >>> Thank you in advanced for your responses. >>> >>> Kind regards, >>> >>> Ali >>> >> -- >> 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 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] Bond breakage modelling
I've never done it myself, so not really. The manual should help :) I don't know if Morse potentials come built-in, or that you'll need to make tables. Be aware that if you have three or more morse potential particles together they can and will form stable triangles, because there is no influence of the angle on the potential. Peter On 19-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how to implement it? > Best regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle dependence on >> the potential energy, since the non-bonded potentials must be pair-wise. >> Depending on the exact problem this may be acceptable though. The angle >> dependence on the potential energy also immediately points out an issue >> with your cut-off based approach: how will you deal with the angle(s)? >> >> In literature I have seen some papers of people pulling proteins apart, >> breaking cystein bridges. Those may contain some insight/ideas. >> >> >> Peter >> >>> On 19-02-19 11:28, Ali Khodayari wrote: >>> Dear All, >>> >>> >>> >>> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted >>> to GROMACS. The model is validated and works properly. >>> >>> We are investigating the behavior of the material under tensile load. >>> However, as covalent bonds are modelled with a harmonic potential -as it is >>> in most of the non-reactive force fields- some parameters cannot be >>> extracted. Is there any way to mimic the breakage of the bonds, let's say >>> when the distance of the atoms exceed a certain amount? In other words, if >>> we have a rough idea of the strain at which bonds break, can GROMACS neglect >>> bonds from a certain cut-off onwards? >>> >>> Thank you in advanced for your responses. >>> >>> Kind regards, >>> >>> Ali >>> >> -- >> 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.
Re: [gmx-users] Bond breakage modelling
Dear Paul, Thank you for your response. Unfortunately, ReaxFF shows some discrepancies in some cases when it comes to carbohydrates. Besides, its parameters are not written for GROMACS. I am looking for maybe a code to mimic this behavior using the validated force fields for carbohydrates, say GROMOS or else. Kind regards, Ali -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of Paul Bauer Sent: dinsdag 19 februari 2019 13:43 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Bond breakage modelling Hello, in general I would advise not to use a classical force field to model a quantum mechanical effect like breaking a bond. Classical force fields are not parametrized to reproduce those effects, and while you might get something that looks fine with the morse potential it would definitely be unphysical. If you want to study quantum effects, use a QM method for the parts that are involved in bond breaking, or use a reactive force field like ReaxFF. Cheers Paul On 2019-02-19 13:35, Ali Khodayari wrote: > Dear Peter, > > Thank you for your prompt reply. > I think I can try the morse potential to see how the system responds. > Could you kindly provide some more info about how to implement it? > Best regards, > Ali > > > >> On 19 Feb 2019, at 11:35, Peter Kroon wrote: >> >> Hi Ali, >> >> >> The short answer is "not really". You could model your bonds as >> non-bonded (morse) potentials, but then you lose all angle dependence >> on the potential energy, since the non-bonded potentials must be pair-wise. >> Depending on the exact problem this may be acceptable though. The >> angle dependence on the potential energy also immediately points out >> an issue with your cut-off based approach: how will you deal with the angle(s)? >> >> In literature I have seen some papers of people pulling proteins >> apart, breaking cystein bridges. Those may contain some insight/ideas. >> >> >> Peter >> >>> On 19-02-19 11:28, Ali Khodayari wrote: >>> Dear All, >>> >>> >>> >>> We have simulated a cellulose fiber using GLYCAM06 ff parameters >>> converted to GROMACS. The model is validated and works properly. >>> >>> We are investigating the behavior of the material under tensile load. >>> However, as covalent bonds are modelled with a harmonic potential >>> -as it is in most of the non-reactive force fields- some parameters >>> cannot be extracted. Is there any way to mimic the breakage of the >>> bonds, let's say when the distance of the atoms exceed a certain >>> amount? In other words, if we have a rough idea of the strain at >>> which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? >>> >>> Thank you in advanced for your responses. >>> >>> Kind regards, >>> >>> Ali >>> >> -- >> Gromacs Users mailing list >> >> * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Readhttp://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 togmx-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 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] Bond breakage modelling
Hello, in general I would advise not to use a classical force field to model a quantum mechanical effect like breaking a bond. Classical force fields are not parametrized to reproduce those effects, and while you might get something that looks fine with the morse potential it would definitely be unphysical. If you want to study quantum effects, use a QM method for the parts that are involved in bond breaking, or use a reactive force field like ReaxFF. Cheers Paul On 2019-02-19 13:35, Ali Khodayari wrote: Dear Peter, Thank you for your prompt reply. I think I can try the morse potential to see how the system responds. Could you kindly provide some more info about how to implement it? Best regards, Ali On 19 Feb 2019, at 11:35, Peter Kroon wrote: Hi Ali, The short answer is "not really". You could model your bonds as non-bonded (morse) potentials, but then you lose all angle dependence on the potential energy, since the non-bonded potentials must be pair-wise. Depending on the exact problem this may be acceptable though. The angle dependence on the potential energy also immediately points out an issue with your cut-off based approach: how will you deal with the angle(s)? In literature I have seen some papers of people pulling proteins apart, breaking cystein bridges. Those may contain some insight/ideas. Peter On 19-02-19 11:28, Ali Khodayari wrote: Dear All, We have simulated a cellulose fiber using GLYCAM06 ff parameters converted to GROMACS. The model is validated and works properly. We are investigating the behavior of the material under tensile load. However, as covalent bonds are modelled with a harmonic potential -as it is in most of the non-reactive force fields- some parameters cannot be extracted. Is there any way to mimic the breakage of the bonds, let's say when the distance of the atoms exceed a certain amount? In other words, if we have a rough idea of the strain at which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? Thank you in advanced for your responses. Kind regards, Ali -- Gromacs Users mailing list * Please search the archive athttp://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Readhttp://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 togmx-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.
Re: [gmx-users] Bond breakage modelling
Dear Peter, Thank you for your prompt reply. I think I can try the morse potential to see how the system responds. Could you kindly provide some more info about how to implement it? Best regards, Ali > On 19 Feb 2019, at 11:35, Peter Kroon wrote: > > Hi Ali, > > > The short answer is "not really". You could model your bonds as > non-bonded (morse) potentials, but then you lose all angle dependence on > the potential energy, since the non-bonded potentials must be pair-wise. > Depending on the exact problem this may be acceptable though. The angle > dependence on the potential energy also immediately points out an issue > with your cut-off based approach: how will you deal with the angle(s)? > > In literature I have seen some papers of people pulling proteins apart, > breaking cystein bridges. Those may contain some insight/ideas. > > > Peter > >> On 19-02-19 11:28, Ali Khodayari wrote: >> Dear All, >> >> >> >> We have simulated a cellulose fiber using GLYCAM06 ff parameters converted >> to GROMACS. The model is validated and works properly. >> >> We are investigating the behavior of the material under tensile load. >> However, as covalent bonds are modelled with a harmonic potential -as it is >> in most of the non-reactive force fields- some parameters cannot be >> extracted. Is there any way to mimic the breakage of the bonds, let's say >> when the distance of the atoms exceed a certain amount? In other words, if >> we have a rough idea of the strain at which bonds break, can GROMACS neglect >> bonds from a certain cut-off onwards? >> >> Thank you in advanced for your responses. >> >> Kind regards, >> >> Ali >> > -- > 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.
Re: [gmx-users] Bond breakage modelling
Hi Ali, The short answer is "not really". You could model your bonds as non-bonded (morse) potentials, but then you lose all angle dependence on the potential energy, since the non-bonded potentials must be pair-wise. Depending on the exact problem this may be acceptable though. The angle dependence on the potential energy also immediately points out an issue with your cut-off based approach: how will you deal with the angle(s)? In literature I have seen some papers of people pulling proteins apart, breaking cystein bridges. Those may contain some insight/ideas. Peter On 19-02-19 11:28, Ali Khodayari wrote: > Dear All, > > > > We have simulated a cellulose fiber using GLYCAM06 ff parameters converted > to GROMACS. The model is validated and works properly. > > We are investigating the behavior of the material under tensile load. > However, as covalent bonds are modelled with a harmonic potential -as it is > in most of the non-reactive force fields- some parameters cannot be > extracted. Is there any way to mimic the breakage of the bonds, let's say > when the distance of the atoms exceed a certain amount? In other words, if > we have a rough idea of the strain at which bonds break, can GROMACS neglect > bonds from a certain cut-off onwards? > > Thank you in advanced for your responses. > > Kind regards, > > Ali > -- 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] Bond breakage modelling
Dear All, We have simulated a cellulose fiber using GLYCAM06 ff parameters converted to GROMACS. The model is validated and works properly. We are investigating the behavior of the material under tensile load. However, as covalent bonds are modelled with a harmonic potential -as it is in most of the non-reactive force fields- some parameters cannot be extracted. Is there any way to mimic the breakage of the bonds, let's say when the distance of the atoms exceed a certain amount? In other words, if we have a rough idea of the strain at which bonds break, can GROMACS neglect bonds from a certain cut-off onwards? Thank you in advanced for your responses. Kind regards, Ali -- 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.
