Re: [gmx-users] Re: BAR calculations with tabulated non-bonded potentials
On 5/20/12 2:30 AM, jrustad wrote: Justin A. Lemkul wrote You don't need the pull code if the two atoms are in the same [moleculetype] - a molecule in Gromacs is any set of atoms; they don't necessarily have to make chemical sense. The only problem I see is that if you have two atoms in the same location, while simultaneously turning one on and the other off, you will likely develop strong repulsive interactions between them such that the constraints may fail and your atoms will be displaced from the desired location. I can't say for sure whether it will be a problem, but if you've got atom A existing at 20% and atom B trying to exist at 80% in the exact same location, that sounds like a recipe for trouble. OK, thanks very much for the advice, however, I'm not following something here- maybe I am just being dense: I thought the point was that the Fe2+ and Fe3+ ions cannot be in the same molecule, because the lookup tables for their short ranged interactions need to be assigned using energygrps, which seem to apply to molecules not atom types. If the tables could be applied to atom types rather than molecules (which makes more sense to me anyway), then there would be no problems. You can assign energygrps to any valid group, though I honestly have no experience using such groups with tables. It may work differently. I thought it was possible in GMX to completely switch off all interactions (including coulomb and vdw) between selected molecules. If so, then when one turns on while the other turns off they never interact, correct? Maybe I am wrong that it is possible to exclude all interactions between two given molecules? Forgive me, the enegrygrp_excl option slipped my mind when I wrote that last message, so yes, it should be possible to exclude their interactions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: BAR calculations with tabulated non-bonded potentials
Thanks- yes, I suspected this might be the case, however, in the context of a free energy calculation it seems difficult to associate the lookup table with a molecule type rather than an atom type. In other words, I have defined a molecule Fe which will change from Fe2 to Fe3. So, its true that the code seems to want a single lookup table to be associated with the molecule from the beginning (rather than an atomtype), which suggests that I can't do what I want to do in a straightforward way. I thought of a possible fix last night- I could define two molecules Fe2 and Fe3, assign lookup tables using energygrps in the normal way. Then I could: (1) turn off the interaction between the two molecules (2) put in a constraint to force them to be on top of each other. Then I could fix things so that as lambda went from 0 1, the Fe2 turns on, and the Fe3 shuts off. -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-calculations-with-tabulated-non-bonded-potentials-tp4993395p4994644.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: BAR calculations with tabulated non-bonded potentials
On 5/19/12 1:13 PM, jrustad wrote: Thanks- yes, I suspected this might be the case, however, in the context of a free energy calculation it seems difficult to associate the lookup table with a molecule type rather than an atom type. In other words, I have defined a molecule Fe which will change from Fe2 to Fe3. So, its true that the code seems to want a single lookup table to be associated with the molecule from the beginning (rather than an atomtype), which suggests that I can't do what I want to do in a straightforward way. I thought of a possible fix last night- I could define two molecules Fe2 and Fe3, assign lookup tables using energygrps in the normal way. Then I could: (1) turn off the interaction between the two molecules (2) put in a constraint to force them to be on top of each other. Then I could fix things so that as lambda went from 0 1, the Fe2 turns on, and the Fe3 shuts off. I don't know how complex the system is you're dealing with, but at this point, isn't it just far more straightforward to construct a rudimentary force field with a few atom types rather than rely on (slow) tabulated functions and potential funny business to get the free energy code to work? -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: BAR calculations with tabulated non-bonded potentials
Justin A. Lemkul wrote I don't know how complex the system is you're dealing with, but at this point, isn't it just far more straightforward to construct a rudimentary force field with a few atom types rather than rely on (slow) tabulated functions and potential funny business to get the free energy code to work? Yes, well, I don't want to invent and validate a whole new forcefield, if that's what you mean. I would sooner write a BAR code from scratch than do that. Do you think the approach above won't work for some reason? Its unusual maybe to set a constraint to zero bond length in the pull code (which I think is the only way in GMX to set constraints between atoms in different molecules). But other than that, it looks straightforward. -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-calculations-with-tabulated-non-bonded-potentials-tp4993395p4994805.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] Re: BAR calculations with tabulated non-bonded potentials
On 5/19/12 5:42 PM, jrustad wrote: Justin A. Lemkul wrote I don't know how complex the system is you're dealing with, but at this point, isn't it just far more straightforward to construct a rudimentary force field with a few atom types rather than rely on (slow) tabulated functions and potential funny business to get the free energy code to work? Yes, well, I don't want to invent and validate a whole new forcefield, if that's what you mean. I would sooner write a BAR code from scratch than do that. Do you think the approach above won't work for some reason? As far as nonbonded interactions go, I was simply suggesting constructing a new force field for better performance. Doing table lookups for all the pairs you listed before will be a serious performance hit. Its unusual maybe to set a constraint to zero bond length in the pull code (which I think is the only way in GMX to set constraints between atoms in different molecules). But other than that, it looks straightforward. You don't need the pull code if the two atoms are in the same [moleculetype] - a molecule in Gromacs is any set of atoms; they don't necessarily have to make chemical sense. The only problem I see is that if you have two atoms in the same location, while simultaneously turning one on and the other off, you will likely develop strong repulsive interactions between them such that the constraints may fail and your atoms will be displaced from the desired location. I can't say for sure whether it will be a problem, but if you've got atom A existing at 20% and atom B trying to exist at 80% in the exact same location, that sounds like a recipe for trouble. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] Re: BAR calculations with tabulated non-bonded potentials
Justin A. Lemkul wrote You don't need the pull code if the two atoms are in the same [moleculetype] - a molecule in Gromacs is any set of atoms; they don't necessarily have to make chemical sense. The only problem I see is that if you have two atoms in the same location, while simultaneously turning one on and the other off, you will likely develop strong repulsive interactions between them such that the constraints may fail and your atoms will be displaced from the desired location. I can't say for sure whether it will be a problem, but if you've got atom A existing at 20% and atom B trying to exist at 80% in the exact same location, that sounds like a recipe for trouble. OK, thanks very much for the advice, however, I'm not following something here- maybe I am just being dense: I thought the point was that the Fe2+ and Fe3+ ions cannot be in the same molecule, because the lookup tables for their short ranged interactions need to be assigned using energygrps, which seem to apply to molecules not atom types. If the tables could be applied to atom types rather than molecules (which makes more sense to me anyway), then there would be no problems. I thought it was possible in GMX to completely switch off all interactions (including coulomb and vdw) between selected molecules. If so, then when one turns on while the other turns off they never interact, correct? Maybe I am wrong that it is possible to exclude all interactions between two given molecules? -- View this message in context: http://gromacs.5086.n6.nabble.com/BAR-calculations-with-tabulated-non-bonded-potentials-tp4993395p4994907.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
