Re: [gmx-users] CHARMM36 for GMX
That's true, a lot of redundant stuff there and once again these are very basic forcefield facts for what biochem folks do. In my case, I have a bunch of very simple situations in crystal structures, but now I gotta use CHARMM or AMBER (lipids!) and charge assignment (half the time perfectly applicable to organic chemistry, yet entirely untouched in this field) in those simple situations becomes a challenge, especially when they control critical physics in the system. All in all, I hate reading detailed FF documentation. However, so as not to post questions like a good 90% of what we see on this board, I'm pretty sure I'll have to with CHARMM. I will do my best not to contribute to the whole "please do my job for me" effort here. :) As I told Mark, it is the developers' fault -- people use the incorrect tool just because it is a great piece of software. Take it as a compliment. As always, thanks. Alex On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul wrote: > > > On 8/2/17 2:52 PM, Alex wrote: > >> Yeah, those are indeed there for the particular molecules, thanks. I >> understand that this is the only way to go, it's just that my use of GMX >> is >> somewhat different in that I rarely use molecules in the normal sense, and >> OPLS-AA, being a LEGO for simple groups, has been very convenient with >> that >> catalog you mentioned. Like, place a carboxyl termination somewhere, or >> have a hole in a bulk sheet of graphene, etc. >> >> > All additive force fields are constructed in the same way, from building > blocks. It's just that OPLS-AA uses a huge amount of (redundant in many > cases) atom types and can be mapped to different charges based on different > situations. It's also why OPLS-AA has separate bonded and nonbonded atom > types. There is greater diversity among nonbonded types but fewer bonded > types, reducing the dimensionality of the internal parameters rather than > having huge amounts of duplicated bonded parameters for types that really > aren't different. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] CHARMM36 for GMX
On 8/2/17 2:52 PM, Alex wrote: Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc. All additive force fields are constructed in the same way, from building blocks. It's just that OPLS-AA uses a huge amount of (redundant in many cases) atom types and can be mapped to different charges based on different situations. It's also why OPLS-AA has separate bonded and nonbonded atom types. There is greater diversity among nonbonded types but fewer bonded types, reducing the dimensionality of the internal parameters rather than having huge amounts of duplicated bonded parameters for types that really aren't different. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Yeah, those are indeed there for the particular molecules, thanks. I understand that this is the only way to go, it's just that my use of GMX is somewhat different in that I rarely use molecules in the normal sense, and OPLS-AA, being a LEGO for simple groups, has been very convenient with that catalog you mentioned. Like, place a carboxyl termination somewhere, or have a hole in a bulk sheet of graphene, etc. In any case, thank you. Alex On Wed, Aug 2, 2017 at 12:41 PM, Justin Lemkul wrote: > > > On 8/2/17 2:38 PM, Alex wrote: > >> Huh. Most of my work has been with OPLS-AA, so I took that for granted. >> Where would the actual charges be, then? >> >> > In the .rtp file, where residues are defined. Charges are not (and should > not) necessarily be linked to atom types; they are a function of > parametrized groups or molecules. > > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] CHARMM36 for GMX
On 8/2/17 2:38 PM, Alex wrote: Huh. Most of my work has been with OPLS-AA, so I took that for granted. Where would the actual charges be, then? In the .rtp file, where residues are defined. Charges are not (and should not) necessarily be linked to atom types; they are a function of parametrized groups or molecules. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Huh. Most of my work has been with OPLS-AA, so I took that for granted. Where would the actual charges be, then? Alex On Wed, Aug 2, 2017 at 12:32 PM, Justin Lemkul wrote: > > > On 8/2/17 2:18 PM, Alex wrote: > >> Hi all, >> >> I am not entirely sure it's a question for the Gromacs community, as this >> is regarding CHARMM36, but it appears that the original forcefield is >> fine, >> while I am confused by its Gromacs version. >> >> Namely this: the MacKerell website distributes a Gromacs version of >> CHARMM36 where ffnonbonded.itp has pretty much all default charges set to >> zero. Is this called for?? >> >> I apologize in advance if this is a dumb or misdirected question, as I've >> never worked with CHARMM before. >> >> > Charges in ffnonbonded.itp are never used by any force field. It's > nothing to do with CHARMM, just a relic of old GROMACS formats and likely a > desire to catalog "default" charges for certain groups. But they serve no > functional purpose. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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] CHARMM36 for GMX
On 8/2/17 2:18 PM, Alex wrote: Hi all, I am not entirely sure it's a question for the Gromacs community, as this is regarding CHARMM36, but it appears that the original forcefield is fine, while I am confused by its Gromacs version. Namely this: the MacKerell website distributes a Gromacs version of CHARMM36 where ffnonbonded.itp has pretty much all default charges set to zero. Is this called for?? I apologize in advance if this is a dumb or misdirected question, as I've never worked with CHARMM before. Charges in ffnonbonded.itp are never used by any force field. It's nothing to do with CHARMM, just a relic of old GROMACS formats and likely a desire to catalog "default" charges for certain groups. But they serve no functional purpose. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] CHARMM36 for GMX
Hi all, I am not entirely sure it's a question for the Gromacs community, as this is regarding CHARMM36, but it appears that the original forcefield is fine, while I am confused by its Gromacs version. Namely this: the MacKerell website distributes a Gromacs version of CHARMM36 where ffnonbonded.itp has pretty much all default charges set to zero. Is this called for?? I apologize in advance if this is a dumb or misdirected question, as I've never worked with CHARMM before. Thank you, 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.
