Re: [gmx-users] Magnetic field in GROMACS
Dear Alex, Thanks for your words. Yes, we have going on research and we look to the future. But we are suffering from the lack of resources. We did some work on electric field code but we could not call the velocity of each particle to do the cross product with the magnetic field and also our coding skills are horrible ;). Thanks On Thu, Jun 21, 2018 at 3:47 AM, Alex wrote: > I would at least first try to hardcode a test Lorentz force for e.g. a > given constant magnetic field to see what happens and whether you can > observe anything fun. > > On an unrelated note, I just want to say that it is great to see that > there is scientific research going on in Iraq after years of war and > destruction. Hats off to you and very best of luck! > > Alex > > > > On 6/21/2018 2:22 AM, حبيبة علي wrote: > >> I thought you are a developer ;) >> I think updating electric field file is not a problem but the >> complicated thing is what are the other files that related to it. Such as >> how to implement it in mdp files which I think need to update different >> files. If there are any analyzing commands need updating, etc >> I will keep trying >> Thanks >> >> >> On Thu, Jun 21, 2018 at 2:24 AM, Alex wrote: >> >> Nah, I'm just a user. ;) >>> >>> What David and I were discussing is not a beginner's task (and I can't >>> see >>> a large number of users for that otherwise awesome functionality), but if >>> you'd like to code the simple vector product, I am pretty sure there will >>> be those who could direct you to the right files. >>> >>> Alex >>> >>> >>> >>> On 6/21/2018 1:08 AM, حبيبة علي wrote: >>> >>> Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed wrote: Hello, > I looked for that before and I tried updating the electric field code > as > both of them are related to Lorentz force. Unfortunately, I failed > because > there are different codes need to be updated. > It would be amazing if the developers participate in this code. > Thanks > Ali > > On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel < > sp...@xray.bmc.uu.se > wrote: > > Den 2018-06-20 kl. 10:20, skrev Alex: > >> David, >> >>> I can think of many realistic cases when looking at the effects of >>> magnetic fields in MD would be of interest, just not in what Gromacs >>> is >>> normally used for. >>> >>> It's just a completely different animal in terms of what causes those >>> effects and Lorentz force applied to point charges would likely be a >>> >>> very >> bad approximation. But in general, an implementation of >> self-consistent >> >>> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. >>> >>> Feel free to open a redmine issue to discuss it there. >>> >> We have an implementation of electric fields that can be used as a >> template. >> >> >> Alex >> >>> >>> >>> Magnetic fields are typically very weak such that they are negligable >>> in >>> >> realistic cases. This is why nobody bothered to implement it. >> >>> -- >>> David van der Spoel, Ph.D., Professor of Biology >> Head of Department, Cell & Molecular Biology, Uppsala University. >> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. >> http://www.icm.uu.se >> -- >> 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. >>> >>> >> >> > -- > Gromacs
Re: [gmx-users] Magnetic field in GROMACS
I would at least first try to hardcode a test Lorentz force for e.g. a given constant magnetic field to see what happens and whether you can observe anything fun. On an unrelated note, I just want to say that it is great to see that there is scientific research going on in Iraq after years of war and destruction. Hats off to you and very best of luck! Alex On 6/21/2018 2:22 AM, حبيبة علي wrote: I thought you are a developer ;) I think updating electric field file is not a problem but the complicated thing is what are the other files that related to it. Such as how to implement it in mdp files which I think need to update different files. If there are any analyzing commands need updating, etc I will keep trying Thanks On Thu, Jun 21, 2018 at 2:24 AM, Alex wrote: Nah, I'm just a user. ;) What David and I were discussing is not a beginner's task (and I can't see a large number of users for that otherwise awesome functionality), but if you'd like to code the simple vector product, I am pretty sure there will be those who could direct you to the right files. Alex On 6/21/2018 1:08 AM, حبيبة علي wrote: Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed wrote: Hello, I looked for that before and I tried updating the electric field code as both of them are related to Lorentz force. Unfortunately, I failed because there are different codes need to be updated. It would be amazing if the developers participate in this code. Thanks Ali On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel < sp...@xray.bmc.uu.se wrote: Den 2018-06-20 kl. 10:20, skrev Alex: David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorentz force applied to point charges would likely be a very bad approximation. But in general, an implementation of self-consistent MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. Feel free to open a redmine issue to discuss it there. We have an implementation of electric fields that can be used as a template. Alex Magnetic fields are typically very weak such that they are negligable in realistic cases. This is why nobody bothered to implement it. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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. -- 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] Magnetic field in GROMACS
I thought you are a developer ;) I think updating electric field file is not a problem but the complicated thing is what are the other files that related to it. Such as how to implement it in mdp files which I think need to update different files. If there are any analyzing commands need updating, etc I will keep trying Thanks On Thu, Jun 21, 2018 at 2:24 AM, Alex wrote: > Nah, I'm just a user. ;) > > What David and I were discussing is not a beginner's task (and I can't see > a large number of users for that otherwise awesome functionality), but if > you'd like to code the simple vector product, I am pretty sure there will > be those who could direct you to the right files. > > Alex > > > > On 6/21/2018 1:08 AM, حبيبة علي wrote: > >> Dear David and Alex, >> >> Thanks for the replies. I'm happy that you will consider it. You are the >> developers and it is clear for you which file should be updated; >> >> Dear Ali, >> My coding skills are very bad and I have no idea which file I need to look >> at. >> >> Best >> >> On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed wrote: >> >> Hello, >>> I looked for that before and I tried updating the electric field code as >>> both of them are related to Lorentz force. Unfortunately, I failed >>> because >>> there are different codes need to be updated. >>> It would be amazing if the developers participate in this code. >>> Thanks >>> Ali >>> >>> On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel < >>> sp...@xray.bmc.uu.se >>> wrote: >>> >>> Den 2018-06-20 kl. 10:20, skrev Alex: David, > > I can think of many realistic cases when looking at the effects of > magnetic fields in MD would be of interest, just not in what Gromacs is > normally used for. > > It's just a completely different animal in terms of what causes those > effects and Lorentz force applied to point charges would likely be a > very >>> bad approximation. But in general, an implementation of self-consistent > MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. > > Feel free to open a redmine issue to discuss it there. We have an implementation of electric fields that can be used as a template. Alex > > > > Magnetic fields are typically very weak such that they are negligable >> > in >>> realistic cases. This is why nobody bothered to implement it. >> >> >> -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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. > -- Habiba Ali, Department of Chemistry, University of Mosul-Iraq -- 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] Magnetic field in GROMACS
Nah, I'm just a user. ;) What David and I were discussing is not a beginner's task (and I can't see a large number of users for that otherwise awesome functionality), but if you'd like to code the simple vector product, I am pretty sure there will be those who could direct you to the right files. Alex On 6/21/2018 1:08 AM, حبيبة علي wrote: Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed wrote: Hello, I looked for that before and I tried updating the electric field code as both of them are related to Lorentz force. Unfortunately, I failed because there are different codes need to be updated. It would be amazing if the developers participate in this code. Thanks Ali On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel Den 2018-06-20 kl. 10:20, skrev Alex: David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorentz force applied to point charges would likely be a very bad approximation. But in general, an implementation of self-consistent MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. Feel free to open a redmine issue to discuss it there. We have an implementation of electric fields that can be used as a template. Alex Magnetic fields are typically very weak such that they are negligable in realistic cases. This is why nobody bothered to implement it. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] Magnetic field in GROMACS
Dear David and Alex, Thanks for the replies. I'm happy that you will consider it. You are the developers and it is clear for you which file should be updated; Dear Ali, My coding skills are very bad and I have no idea which file I need to look at. Best On Wed, Jun 20, 2018 at 12:02 PM, Ali Ahmed wrote: > Hello, > I looked for that before and I tried updating the electric field code as > both of them are related to Lorentz force. Unfortunately, I failed because > there are different codes need to be updated. > It would be amazing if the developers participate in this code. > Thanks > Ali > > On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel > > wrote: > > > Den 2018-06-20 kl. 10:20, skrev Alex: > > > >> David, > >> > >> I can think of many realistic cases when looking at the effects of > >> magnetic fields in MD would be of interest, just not in what Gromacs is > >> normally used for. > >> > >> It's just a completely different animal in terms of what causes those > >> effects and Lorentz force applied to point charges would likely be a > very > >> bad approximation. But in general, an implementation of self-consistent > >> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. > >> > > > > Feel free to open a redmine issue to discuss it there. > > We have an implementation of electric fields that can be used as a > > template. > > > > > >> Alex > >> > >> > >> > >>> Magnetic fields are typically very weak such that they are negligable > in > >>> realistic cases. This is why nobody bothered to implement it. > >>> > >>> > >> > > > > -- > > David van der Spoel, Ph.D., Professor of Biology > > Head of Department, Cell & Molecular Biology, Uppsala University. > > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > > http://www.icm.uu.se > > -- > > 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. > -- Habiba Ali, Department of Chemistry, University of Mosul-Iraq -- 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] Magnetic field in GROMACS
Hello, I looked for that before and I tried updating the electric field code as both of them are related to Lorentz force. Unfortunately, I failed because there are different codes need to be updated. It would be amazing if the developers participate in this code. Thanks Ali On Wed, Jun 20, 2018 at 3:28 AM, David van der Spoel wrote: > Den 2018-06-20 kl. 10:20, skrev Alex: > >> David, >> >> I can think of many realistic cases when looking at the effects of >> magnetic fields in MD would be of interest, just not in what Gromacs is >> normally used for. >> >> It's just a completely different animal in terms of what causes those >> effects and Lorentz force applied to point charges would likely be a very >> bad approximation. But in general, an implementation of self-consistent >> MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. >> > > Feel free to open a redmine issue to discuss it there. > We have an implementation of electric fields that can be used as a > template. > > >> Alex >> >> >> >>> Magnetic fields are typically very weak such that they are negligable in >>> realistic cases. This is why nobody bothered to implement it. >>> >>> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Head of Department, Cell & Molecular Biology, Uppsala University. > Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. > http://www.icm.uu.se > -- > 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] Magnetic field in GROMACS
Den 2018-06-20 kl. 10:20, skrev Alex: David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorentz force applied to point charges would likely be a very bad approximation. But in general, an implementation of self-consistent MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. Feel free to open a redmine issue to discuss it there. We have an implementation of electric fields that can be used as a template. Alex Magnetic fields are typically very weak such that they are negligable in realistic cases. This is why nobody bothered to implement it. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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] Magnetic field in GROMACS
David, I can think of many realistic cases when looking at the effects of magnetic fields in MD would be of interest, just not in what Gromacs is normally used for. It's just a completely different animal in terms of what causes those effects and Lorentz force applied to point charges would likely be a very bad approximation. But in general, an implementation of self-consistent MD+FDTD (i.e. MD + Maxwell's eqns) would be pretty amazing. Alex Magnetic fields are typically very weak such that they are negligable in realistic cases. This is why nobody bothered to implement it. -- 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] Magnetic field in GROMACS
Den 2018-06-20 kl. 09:26, skrev حبيبة علي: Dear Dr. David, I'm Habiba, I just start learning GROMACS and I'm going to apply magnetic field on my system which is polymer. I looked online then I noticed its not implemented in GROMACS but, people are talking about it. You shared all GROMACS package and no body shares magnetic implementation with us. Pleas, can you help me on how to apply it? Best! -- Habiba Ali, Department of Chemistry, University of Mosul-Iraq Please ask further questions on the mailing list. Magnetic fields are typically very weak such that they are negligable in realistic cases. This is why nobody bothered to implement it. -- David van der Spoel, Ph.D., Professor of Biology Head of Department, Cell & Molecular Biology, Uppsala University. Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205. http://www.icm.uu.se -- 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.
