Re: [gmx-users] how to mimick explicit hydrogen bonding
Mark Abraham ha scritto: ms wrote: Ok, the problem is that I want to re-implement a quite minimal coarse-grained FF (so no explicit solvent etc.) and a directional interaction would be useful. Well you should consider alternative software, then. I see. I wonder if patching gmx to do that is possible/difficult, however (I'm not confident at all in doing that, but I know closely people who are). IIRC, CHARMM did have explicit H-bond models ages ago, but (again IIRC) they're not in the modern versions and not in the upcoming GROMACS port. Ok, thanks for clarifying! Thanks, M. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to mimick explicit hydrogen bonding
Hi Mark, Thanks for your answer. Mark Abraham ha scritto: There's nothing directional about the physics of a hydrogen bond, unless your model makes it so. There'd be nothing intrinsically valid or invalid with that either, so long as you parameterized the force field under that assumption. If using rigid water models and/or other atomic constraints where H-bonded atoms can't have a geometric distortion, I suppose such a model might be necessary. It's still far from clear that H-bonding is sufficiently different from other electrostatic interactions to warrant special treatment (and thus reparameterization of charges). Ok, the problem is that I want to re-implement a quite minimal coarse-grained FF (so no explicit solvent etc.) and a directional interaction would be useful. Can anyone give me hints on how to describe a directional hydrogen-bond-like interaction? You would not achieve this in GROMACS without code modification. A special non-bonded list for H-bonded water (and maybe H-bonded non-water) that didn't call the standard water inner loops would be required. I see. I asked because I think I've read that there were force fields with explicit hydrogen bond treatment (some CHARMM?) that were imported into Gromacs, and I thought there was some clever hack to get it working -but I guess that it is not the case. Thanks! m. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to mimick explicit hydrogen bonding
ms wrote: Hi Mark, Thanks for your answer. Mark Abraham ha scritto: There's nothing directional about the physics of a hydrogen bond, unless your model makes it so. There'd be nothing intrinsically valid or invalid with that either, so long as you parameterized the force field under that assumption. If using rigid water models and/or other atomic constraints where H-bonded atoms can't have a geometric distortion, I suppose such a model might be necessary. It's still far from clear that H-bonding is sufficiently different from other electrostatic interactions to warrant special treatment (and thus reparameterization of charges). Ok, the problem is that I want to re-implement a quite minimal coarse-grained FF (so no explicit solvent etc.) and a directional interaction would be useful. Well you should consider alternative software, then. Can anyone give me hints on how to describe a directional hydrogen-bond-like interaction? You would not achieve this in GROMACS without code modification. A special non-bonded list for H-bonded water (and maybe H-bonded non-water) that didn't call the standard water inner loops would be required. I see. I asked because I think I've read that there were force fields with explicit hydrogen bond treatment (some CHARMM?) that were imported into Gromacs, and I thought there was some clever hack to get it working -but I guess that it is not the case. IIRC, CHARMM did have explicit H-bond models ages ago, but (again IIRC) they're not in the modern versions and not in the upcoming GROMACS port. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to mimick explicit hydrogen bonding
Hi, I need to implement a FF which includes directional hydrogen bonding. It seems however, to my understanding, that Gromacs has no simple way to include an explicitly directional contribution. All I can find is that, in standard force fields, h-bond terms are implicitly described by coulombic and vdw interactions, but I am a bit puzzled by how these terms are combined to give a directional interaction. Can anyone give me hints on how to describe a directional hydrogen-bond-like interaction? thanks! m. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to mimick explicit hydrogen bonding
ms wrote: Hi, I need to implement a FF which includes directional hydrogen bonding. It seems however, to my understanding, that Gromacs has no simple way to include an explicitly directional contribution. All I can find is that, in standard force fields, h-bond terms are implicitly described by coulombic and vdw interactions, but I am a bit puzzled by how these terms are combined to give a directional interaction. There's nothing directional about the physics of a hydrogen bond, unless your model makes it so. There'd be nothing intrinsically valid or invalid with that either, so long as you parameterized the force field under that assumption. If using rigid water models and/or other atomic constraints where H-bonded atoms can't have a geometric distortion, I suppose such a model might be necessary. It's still far from clear that H-bonding is sufficiently different from other electrostatic interactions to warrant special treatment (and thus reparameterization of charges). Can anyone give me hints on how to describe a directional hydrogen-bond-like interaction? You would not achieve this in GROMACS without code modification. A special non-bonded list for H-bonded water (and maybe H-bonded non-water) that didn't call the standard water inner loops would be required. MArk ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
