Re: [gmx-users] Problem with constraints in NVT calculations.
On 10/14/14 7:40 AM, Kester Wong wrote: Hi Justin and all, > > > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > > example I came across is from the work by Ho and Striolo > > > > > > titled: Polarizability effects in molecular dynamics simulations of the > > > graphene-water interface > > > > > > > Of course you can implement whatever you like. Gromacs has been able to carry > > out polarizable simulations for a very long time; I've only ever cautioned > > against abuse of certain models. > > > > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > > polarisable calcs, they are prone to polarisation catastrophe due to the > > massless shells and thermostat instability? > > Polarization catastrophe is possible in any polarizable simulation. Usually > very small time steps are required to avoid this, unless using an anharmonic > potential or a hard wall restraint. > > > Using Morse = yes for the anharmonic potential option, whereas using the > parameters below for the hard wall restraint option? > > pbc = xy > nwall = 2 > wall-atomtype =; optional > wall-type = 12-6 > wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run > wall-density = 5 5 > wall-ewald-zfac = 3 > No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). Although the wall settings have nothing to do with polarisation catastrophe, I guess it might be useful in the following case: I have been using a time step of 1 fs, which is small already, yet the water droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the z-direction. I will try using the wall setup as above, hoping that water remains a droplet with the presence of H3O and Cl ions. Could you please explain what is the difference between the three types of wall; 9-3, 10-4, and 12-6? The exponents used in the LJ potential for the wall. 12-6 is the "normal" LJ potential. The only part of the GROMACS 5.0 manual that described anharmonic bond potential is in the Morse potential section 4.2.2. Like I said, it's not documented. See src/gromacs/gmxlib.c, function anharm_polarize(). Which function is not available in GROMACS yet? What we call the "hard wall" restraint, that reflects a Drude particle along the bond vector connecting it to its parent atom. It prevents the Drude from moving more than a specified amount, thus vastly improving integration stability. See the Appendix of dx.doi.org/10.1021/jp402860e. > > In the paper mentioned above, the authors have carried out three types of cals: > > i) SPC/E on non-pol graphene > > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > > charge): graphene-DP in neutral or charged states > > > > They seemed to have simulated their systems using both additive and polarisable > > (0.878 angstrom^3) models? > > I guess this is where I got confused. > > I suppose you can make any model work if you parametrize it a certain way, but > my point in the previous message is that you shouldn't go off trying to build a > force field that has SWM4-NDP water around additive CHARMM solutes. > > > Yep, now I understand it. > If I wanted to also describe graphene, is it possible to include carbon > parameters in the SWM4-NDP force field then? > Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. That is great! To create a FF that describes the SWM4 water, NDP ions, and graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded parameters, and the LJ nonbonding interaction parameters, is that right? Yes. -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/Mailin
Re: [gmx-users] Problem with constraints in NVT calculations.
Hi Justin and all,> > > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > > example I came across is from the work by Ho and Striolo > > > > > > titled: Polarizability effects in molecular dynamics simulations of the > > > graphene-water interface > > > > > > > Of course you can implement whatever you like. Gromacs has been able to carry > > out polarizable simulations for a very long time; I've only ever cautioned > > against abuse of certain models. > > > > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > > polarisable calcs, they are prone to polarisation catastrophe due to the > > massless shells and thermostat instability? > > Polarization catastrophe is possible in any polarizable simulation. Usually > very small time steps are required to avoid this, unless using an anharmonic > potential or a hard wall restraint. > > > Using Morse = yes for the anharmonic potential option, whereas using the > parameters below for the hard wall restraint option? > > pbc = xy > nwall = 2 > wall-atomtype =; optional > wall-type = 12-6 > wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run > wall-density = 5 5 > wall-ewald-zfac = 3 > No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). Although the wall settings have nothing to do with polarisation catastrophe, I guess it might be useful in the following case: I have been using a time step of 1 fs, which is small already, yet the water droplet (on graphene) quickly fills up the vacuum of ~5-6 nm along the z-direction. I will try using the wall setup as above, hoping that water remains a droplet with the presence of H3O and Cl ions. Could you please explain what is the difference between the three types of wall; 9-3, 10-4, and 12-6?The only part of the GROMACS 5.0 manual that described anharmonic bond potential is in the Morse potential section 4.2.2.Which function is not available in GROMACS yet?> > In the paper mentioned above, the authors have carried out three types of cals: > > i) SPC/E on non-pol graphene > > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > > charge): graphene-DP in neutral or charged states > > > > They seemed to have simulated their systems using both additive and polarisable > > (0.878 angstrom^3) models? > > I guess this is where I got confused. > > I suppose you can make any model work if you parametrize it a certain way, but > my point in the previous message is that you shouldn't go off trying to build a > force field that has SWM4-NDP water around additive CHARMM solutes. > > > Yep, now I understand it. > If I wanted to also describe graphene, is it possible to include carbon > parameters in the SWM4-NDP force field then? > Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. That is great! To create a FF that describes the SWM4 water, NDP ions, and graphene carbon (CA); I will have to include graphene.itp, the CA-CA bonded parameters, and the LJ nonbonding interaction parameters, is that right? > > > > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > > instead of shelltype particle). > > > > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > > can it be replaced with an atom (assuming an induced dipole model) instead of > > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > > opposite charge of the water oxygen atom? > > > > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > > atoms. There's nothing conceptually special about them, we just handle them > > slightly differently in the code. > > > > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > > to experiment if I can: > > i) replace the Drudes to atom with the same configuration - opposite charge, > > mass (0.4 amu), lengths, etc > > > > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise h
Re: [gmx-users] Problem with constraints in NVT calculations.
On 10/10/14 4:59 AM, Kester Wong wrote: Hi Justin and all, > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamics simulations of the > > graphene-water interface > > > > Of course you can implement whatever you like. Gromacs has been able to carry > out polarizable simulations for a very long time; I've only ever cautioned > against abuse of certain models. > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > polarisable calcs, they are prone to polarisation catastrophe due to the > massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint. Using Morse = yes for the anharmonic potential option, whereas using the parameters below for the hard wall restraint option? pbc = xy nwall = 2 wall-atomtype =; optional wall-type = 12-6 wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. run wall-density = 5 5 wall-ewald-zfac = 3 No. I'm not suggesting a Morse potential. What I was referring to was an anharmonic function for the bonds, which is present in Gromacs but I'm not sure if it's documented. The wall settings in Gromacs have nothing to do with this. Such a function is not present in Gromacs (yet). > In the paper mentioned above, the authors have carried out three types of cals: > i) SPC/E on non-pol graphene > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > charge): graphene-DP in neutral or charged states > > They seemed to have simulated their systems using both additive and polarisable > (0.878 angstrom^3) models? > I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes. Yep, now I understand it. If I wanted to also describe graphene, is it possible to include carbon parameters in the SWM4-NDP force field then? Well, strictly speaking, you're not introducing graphene into a SWM4-NDP force field, you're creating a force field that describes both. This can certainly be done if you have all the parameters. > > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > instead of shelltype particle). > > > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > can it be replaced with an atom (assuming an induced dipole model) instead of > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > opposite charge of the water oxygen atom? > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > atoms. There's nothing conceptually special about them, we just handle them > slightly differently in the code. > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > to experiment if I can: > i) replace the Drudes to atom with the same configuration - opposite charge, > mass (0.4 amu), lengths, etc > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried out differently, so no, this sort of hacked approach probably isn't very robust. You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30? As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right? Right. To relax a system containing Drude particles, is md=steep enough, or the more accurate conjugate gradient? I get unreasonable energy minimised confout.gro structure very often, if there are Drude-based ions included (head-scratching). This suggests either unstable topology or inadequate minimizer. Steepest descent should usually be good enough, if the emtol is set appropriately. > OR > > ii) switch to the more stable SWM4-DP with the hydronium and hydroxide > implementation f
Re: [gmx-users] Problem with constraints in NVT calculations.
Hi Justin and all, > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamics simulations of the > > graphene-water interface > > > > Of course you can implement whatever you like. Gromacs has been able to carry > out polarizable simulations for a very long time; I've only ever cautioned > against abuse of certain models. > > > I guess that GROMACS is capable in running polarisable sims, but for the Drude > polarisable calcs, they are prone to polarisation catastrophe due to the > massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint. Using Morse = yes for the anharmonic potential option, whereas using the parameters below for the hard wall restraint option?pbc = xynwall = 2wall-atomtype = ; optionalwall-type = 12-6wall-r-linpot = 1 ; having a positive val. is esp. useful in equil. runwall-density = 5 5wall-ewald-zfac = 3> In the paper mentioned above, the authors have carried out three types of cals: > i) SPC/E on non-pol graphene > ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states > iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite > charge): graphene-DP in neutral or charged states > > They seemed to have simulated their systems using both additive and polarisable > (0.878 angstrom^3) models? > I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes. Yep, now I understand it. If I wanted to also describe graphene, is it possible to include carbon parameters in the SWM4-NDP force field then?> > On the side: From my previous calcs using GRAPPA force field (TIPS3P water > model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water > into thin layer. But that was polarisable graphene in a rigid rod model (dummy > instead of shelltype particle). > > > > > > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > > can it be replaced with an atom (assuming an induced dipole model) instead of > > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > > opposite charge of the water oxygen atom? > > > > In the Drude model with 0.4-amu particles, the Drudes are essentially just > atoms. There's nothing conceptually special about them, we just handle them > slightly differently in the code. > > > Well since domain decomposition will not work on shelltype calcs, I am intrigued > to experiment if I can: > i) replace the Drudes to atom with the same configuration - opposite charge, > mass (0.4 amu), lengths, etc > The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried out differently, so no, this sort of hacked approach probably isn't very robust. You mean the relaxation during NVT, e.g. emtol = 0.1 and niter = 30?As far as I know, for pure energy minimisation, the shells are treated just like any other particles, so what matters is the shell minimiser/integration differs than an "atom" during MD right?To relax a system containing Drude particles, is md=steep enough, or the more accurate conjugate gradient?I get unreasonable energy minimised confout.gro structure very often, if there are Drude-based ions included (head-scratching).> OR > > ii) switch to the more stable SWM4-DP with the hydronium and hydroxide > implementation from David van der Spoel? I don't know how this relates to the point above about graphene, so I'm a bit lost. SWM4-NDP is a better model than SWM4-DP, FWIW. Absolutely, no doubt about that; SWM4-NDP describes water surf.tension better than SWM4-DP.It was just a thought, that if SWM4-NDP becomes very unstable upon the inclusion of polarisable ions (e.g. hydronium and hydroxide that also contain Drude particle), SWM4-DP could be an alternative? > > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > > example I came across is from the work by Ho and Striolo > > > > titled: Polarizability effects in molecular dynamics simulations of the > > graphene-water interface > > > > Of course you can implement whatever you like. Gromacs has been able to carry > out polarizable simulations for a very long time; I've only ever cautioned > against abuse of ce
Re: [gmx-users] Problem with constraints in NVT calculations.
On 10/8/14 8:57 AM, Kester Wong wrote: Hi Justin, > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > example I came across is from the work by Ho and Striolo > > titled: Polarizability effects in molecular dynamics simulations of the > graphene-water interface > Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models. I guess that GROMACS is capable in running polarisable sims, but for the Drude polarisable calcs, they are prone to polarisation catastrophe due to the massless shells and thermostat instability? Polarization catastrophe is possible in any polarizable simulation. Usually very small time steps are required to avoid this, unless using an anharmonic potential or a hard wall restraint. In the paper mentioned above, the authors have carried out three types of cals: i) SPC/E on non-pol graphene ii) SWM4-DP on non-pol graphene: graphene in neutral or charged states iii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite charge): graphene-DP in neutral or charged states They seemed to have simulated their systems using both additive and polarisable (0.878 angstrom^3) models? I guess this is where I got confused. I suppose you can make any model work if you parametrize it a certain way, but my point in the previous message is that you shouldn't go off trying to build a force field that has SWM4-NDP water around additive CHARMM solutes. On the side: From my previous calcs using GRAPPA force field (TIPS3P water model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water into thin layer. But that was polarisable graphene in a rigid rod model (dummy instead of shelltype particle). > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > can it be replaced with an atom (assuming an induced dipole model) instead of > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > opposite charge of the water oxygen atom? > In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code. Well since domain decomposition will not work on shelltype calcs, I am intrigued to experiment if I can: i) replace the Drudes to atom with the same configuration - opposite charge, mass (0.4 amu), lengths, etc The problem is that shells/Drudes have to be relaxed (SCF) or otherwise have their positions integrated (extended Lagrangian) separately from "normal" atoms. Conceptually, a 0.4-amu Drude is just an atom, but the integration is carried out differently, so no, this sort of hacked approach probably isn't very robust. OR ii) switch to the more stable SWM4-DP with the hydronium and hydroxide implementation from David van der Spoel? I don't know how this relates to the point above about graphene, so I'm a bit lost. SWM4-NDP is a better model than SWM4-DP, FWIW. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Problem with constraints in NVT calculations.
Hi Justin, > Meanwhile, is it possible to implement a self-consistent FF from scratch? One > example I came across is from the work by Ho and Striolo > > titled: Polarizability effects in molecular dynamics simulations of the > graphene-water interface > Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models. I guess that GROMACS is capable in running polarisable sims, but for the Drude polarisable calcs, they are prone to polarisation catastrophe due to the massless shells and thermostat instability?In the paper mentioned above, the authors have carried out three types of cals:i) SPC/E on non-pol graphene ii) SWM4-DP on non-pol graphene: graphene in neutral or charged statesiii) SWM4-DP on graphene-DP (one Drude particle per C-atom with opposite charge): graphene-DP in neutral or charged statesThey seemed to have simulated their systems using both additive and polarisable (0.878 angstrom^3) models?I guess this is where I got confused. On the side: From my previous calcs using GRAPPA force field (TIPS3P water model), graphene's polarisation (0.91 angstrom^3) resulted in spreading of water into thin layer. But that was polarisable graphene in a rigid rod model (dummy instead of shelltype particle). > > Pardon me if this sounds outright wrong; regarding the massless Drude particle, > can it be replaced with an atom (assuming an induced dipole model) instead of > the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an > opposite charge of the water oxygen atom? > In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code. Well since domain decomposition will not work on shelltype calcs, I am intrigued to experiment if I can:i) replace the Drudes to atom with the same configuration - opposite charge, mass (0.4 amu), lengths, etcOR ii) switch to the more stable SWM4-DP with the hydronium and hydroxide implementation from David van der Spoel?Regards,Kester -- 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] Problem with constraints in NVT calculations.
On 10/7/14 10:59 PM, Kester Wong wrote: Hi Justin, Thank you for the clarification. I should look into using NAMD. The new polarisable Drude implementation will surely benefit everyone in the MD community. I am looking forward to using it, as with others (I think there was a similar post by Yana Tsoneva on this issue too, dated back in July). Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interface Of course you can implement whatever you like. Gromacs has been able to carry out polarizable simulations for a very long time; I've only ever cautioned against abuse of certain models. Pardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom? In the Drude model with 0.4-amu particles, the Drudes are essentially just atoms. There's nothing conceptually special about them, we just handle them slightly differently in the code. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Problem with constraints in NVT calculations.
Hi Justin, Thank you for the clarification. I should look into using NAMD.The new polarisable Drude implementation will surely benefit everyone in the MD community.I am looking forward to using it, as with others (I think there was a similar post by Yana Tsoneva on this issue too, dated back in July).Meanwhile, is it possible to implement a self-consistent FF from scratch? One example I came across is from the work by Ho and Striolo titled: Polarizability effects in molecular dynamics simulations of the graphene-water interfacePardon me if this sounds outright wrong; regarding the massless Drude particle, can it be replaced with an atom (assuming an induced dipole model) instead of the charge-on-spring model? The mass of the atom can be set to 0.4 amu with an opposite charge of the water oxygen atom?Regards,Kester- 원본 메일 -보낸사람 : Justin Lemkul 받는사람 : 받은날짜 : 2014년 10월 8일(수) 03:02:12제목 : Re: [gmx-users] Problem with constraints in NVT calculations. On 10/6/14 10:35 PM, Kester Wong wrote: > Dear Justin and all, > > > 원본 메일 - > > *보낸사람* : Justin Lemkul > *받는사람* : > *받은날짜* : 2014년 9월 29일(월) 21:32:13 > *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. > > On 9/29/14 8:01 AM, Kester Wong wrote: > > Dear all, > > > > > > I have been using the SWM4-NDP water model that works well with CHARMM27 force > > field. > > > > Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive > force field. The two are not compatible. If you're using them together, you're > basically just gambling that they work. You shouldn't do this. > > Thank you for the information. Actually, I took the data from the > ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I > realised that it does not work like that. > > > If the ffnonbonded.itp file contains the appropriate nonbonded parameters for > the polarisable water model (i.e. the atomtypes and dummies for the Drude water > and ions model), will it work? > > Below is my input topologies: > > https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing No, this is fundamentally wrong. You can't simply combine some additive components and some polarizable components and hope for a sensible physical model. Force fields are derived in self-consistent ways. You can't patch them together. > > > The force field (most recent version) was obtained from virtualchemistry, and > > consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. > > > > The water on graphene (energy minimisation and NVT) calculations are stable, and > > have produced a few NVT runs of up to 10ns. > > > > I also compared the NVT runs with other previously calculated structures, > > namely, the visualised NVT runs are very much comparable to that obtained by > > CHARMM27 force field with TIPS3P water model. > > > > > > However, as the polarisable H3O+ and Cl- ions are inserted into the simulation > > box, the NVT run tends to crash as a result of too many LINCS warnings. > > > > I suspect that the constraints in the H3O is the cause of the LINCS warnings, > > and after removing the [ constraints ] in the topology file, the calculation > > seems to be running. > > > > > > ;[ constraints ] > > > > ;; i funct doh dhh > > > > ;1 3 1 0.102 > > > > ;1 4 1 0.102 > > > > ;1 5 1 0.102 > > > > ;3 4 1 0.169124 > > > > ;4 5 1 0.169124 > > > > ;3 5 1 0.169124 > > > > > > > > Can anyone please tell me if what I am doing is correct? > > > > As I am not sure if removing the H3O constraints in the NVT run is appropriate. > > > > > > With regard to the massless Drude and standard oxygen mass (thank you Justin for > > providing the information), I would like to know why are they not appropriate > > (as mentioned in the previous email) for the SWM4-NDP model? > > > > I wasn't making a declarative statement that it won't work. I was asking > whether anyone had verified that using a massless Drude in that model actually > reproduced all of the physical properties of the SWM4-NDP model. We do all of > our development on the Drude FF with D
Re: [gmx-users] Problem with constraints in NVT calculations.
On 10/6/14 10:35 PM, Kester Wong wrote: Dear Justin and all, 원본 메일 - *보낸사람* : Justin Lemkul *받는사람* : *받은날짜* : 2014년 9월 29일(월) 21:32:13 *제목* : Re: [gmx-users] Problem with constraints in NVT calculations. On 9/29/14 8:01 AM, Kester Wong wrote: > Dear all, > > > I have been using the SWM4-NDP water model that works well with CHARMM27 force > field. > Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, you're basically just gambling that they work. You shouldn't do this. Thank you for the information. Actually, I took the data from the ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I realised that it does not work like that. If the ffnonbonded.itp file contains the appropriate nonbonded parameters for the polarisable water model (i.e. the atomtypes and dummies for the Drude water and ions model), will it work? Below is my input topologies: https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing No, this is fundamentally wrong. You can't simply combine some additive components and some polarizable components and hope for a sensible physical model. Force fields are derived in self-consistent ways. You can't patch them together. > The force field (most recent version) was obtained from virtualchemistry, and > consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. > > The water on graphene (energy minimisation and NVT) calculations are stable, and > have produced a few NVT runs of up to 10ns. > > I also compared the NVT runs with other previously calculated structures, > namely, the visualised NVT runs are very much comparable to that obtained by > CHARMM27 force field with TIPS3P water model. > > > However, as the polarisable H3O+ and Cl- ions are inserted into the simulation > box, the NVT run tends to crash as a result of too many LINCS warnings. > > I suspect that the constraints in the H3O is the cause of the LINCS warnings, > and after removing the [ constraints ] in the topology file, the calculation > seems to be running. > > > ;[ constraints ] > > ;; i funct doh dhh > > ;1 3 1 0.102 > > ;1 4 1 0.102 > > ;1 5 1 0.102 > > ;3 4 1 0.169124 > > ;4 5 1 0.169124 > > ;3 5 1 0.169124 > > > > Can anyone please tell me if what I am doing is correct? > > As I am not sure if removing the H3O constraints in the NVT run is appropriate. > > > With regard to the massless Drude and standard oxygen mass (thank you Justin for > providing the information), I would like to know why are they not appropriate > (as mentioned in the previous email) for the SWM4-NDP model? > I wasn't making a declarative statement that it won't work. I was asking whether anyone had verified that using a massless Drude in that model actually reproduced all of the physical properties of the SWM4-NDP model. We do all of our development on the Drude FF with Drudes of mass = 0.4 amu and the extended Lagrangian. I don't know how a massless Drude behaves in this model. It may work fine, but you should very rigorously verify this yourself before doing anything by doing simulations of pure water. -Justin I have Read the paper by Jochen Hub et al [Chem. Sci., 5, 1745 2013], that their calculated data (water with ions) are in line with experimental results. Upon further inspection, I found more papers that reported the use of 0.4 amu mass and an extended Lagrangian for the Drude particle. e.g. by Yu et al. [J. CHem. Theory Comput. 6, 774-786 2010]. Could you please advise if there is anything I could do, to make the additive and polarisable FFs usable after modification? No. Either the force field must be entirely polarizable or entirely additive. I am more than willing to go through the necessary changes/implementation if it can be done as this is the only avenue that I have left. I am working on the code-level implementation of all the necessary algorithms so people can use our fully polarizable biomolecular FFs for proteins, DNA, water, and ions. It's not a trivial task. I have only a few more hang-ups to work out, but at this point, if you want to be doing polarizable simulations with our FFs, you should look at NAMD. It supports everything you need. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirs
Re: [gmx-users] Problem with constraints in NVT calculations.
Dear Justin and all, 원본 메일 -보낸사람 : Justin Lemkul 받는사람 : 받은날짜 : 2014년 9월 29일(월) 21:32:13제목 : Re: [gmx-users] Problem with constraints in NVT calculations.On 9/29/14 8:01 AM, Kester Wong wrote: > Dear all, > > > I have been using the SWM4-NDP water model that works well with CHARMM27 force > field. > Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, you're basically just gambling that they work. You shouldn't do this. Thank you for the information. Actually, I took the data from the ff-drude-water-ions.itp file and included them in the CHARMM27 itp files. Now I realised that it does not work like that.If the ffnonbonded.itp file contains the appropriate nonbonded parameters for the polarisable water model (i.e. the atomtypes and dummies for the Drude water and ions model), will it work? Below is my input topologies:https://drive.google.com/file/d/0B7ym8d6G9-e2dmdQOHNaU3c3Qkk/view?usp=sharing> The force field (most recent version) was obtained from virtualchemistry, and > consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. > > The water on graphene (energy minimisation and NVT) calculations are stable, and > have produced a few NVT runs of up to 10ns. > > I also compared the NVT runs with other previously calculated structures, > namely, the visualised NVT runs are very much comparable to that obtained by > CHARMM27 force field with TIPS3P water model. > > > However, as the polarisable H3O+ and Cl- ions are inserted into the simulation > box, the NVT run tends to crash as a result of too many LINCS warnings. > > I suspect that the constraints in the H3O is the cause of the LINCS warnings, > and after removing the [ constraints ] in the topology file, the calculation > seems to be running. > > > ;[ constraints ] > > ;; i funct doh dhh > > ;1 3 1 0.102 > > ;1 4 1 0.102 > > ;1 5 1 0.102 > > ;3 4 1 0.169124 > > ;4 5 1 0.169124 > > ;3 5 1 0.169124 > > > > Can anyone please tell me if what I am doing is correct? > > As I am not sure if removing the H3O constraints in the NVT run is appropriate. > > > With regard to the massless Drude and standard oxygen mass (thank you Justin for > providing the information), I would like to know why are they not appropriate > (as mentioned in the previous email) for the SWM4-NDP model? > I wasn't making a declarative statement that it won't work. I was asking whether anyone had verified that using a massless Drude in that model actually reproduced all of the physical properties of the SWM4-NDP model. We do all of our development on the Drude FF with Drudes of mass = 0.4 amu and the extended Lagrangian. I don't know how a massless Drude behaves in this model. It may work fine, but you should very rigorously verify this yourself before doing anything by doing simulations of pure water. -Justin I have Read the paper by Jochen Hub et al [Chem. Sci., 5, 1745 2013], that their calculated data (water with ions) are in line with experimental results.Upon further inspection, I found more papers that reported the use of 0.4 amu mass and an extended Lagrangian for the Drude particle. e.g. by Yu et al. [J. CHem. Theory Comput. 6, 774-786 2010]. Could you please advise if there is anything I could do, to make the additive and polarisable FFs usable after modification?I am more than willing to go through the necessary changes/implementation if it can be done as this is the only avenue that I have left. Thank you in advance.Regards,Kester-- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Problem with constraints in NVT calculations.
On 9/29/14 8:01 AM, Kester Wong wrote: Dear all, I have been using the SWM4-NDP water model that works well with CHARMM27 force field. Time out. SWM4-NDP is a polarizable water model, and CHARMM27 is an additive force field. The two are not compatible. If you're using them together, you're basically just gambling that they work. You shouldn't do this. The force field (most recent version) was obtained from virtualchemistry, and consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al. The water on graphene (energy minimisation and NVT) calculations are stable, and have produced a few NVT runs of up to 10ns. I also compared the NVT runs with other previously calculated structures, namely, the visualised NVT runs are very much comparable to that obtained by CHARMM27 force field with TIPS3P water model. However, as the polarisable H3O+ and Cl- ions are inserted into the simulation box, the NVT run tends to crash as a result of too many LINCS warnings. I suspect that the constraints in the H3O is the cause of the LINCS warnings, and after removing the [ constraints ] in the topology file, the calculation seems to be running. ;[ constraints ] ;; i funct doh dhh ;1 3 1 0.102 ;1 4 1 0.102 ;1 5 1 0.102 ;3 4 1 0.169124 ;4 5 1 0.169124 ;3 5 1 0.169124 Can anyone please tell me if what I am doing is correct? As I am not sure if removing the H3O constraints in the NVT run is appropriate. With regard to the massless Drude and standard oxygen mass (thank you Justin for providing the information), I would like to know why are they not appropriate (as mentioned in the previous email) for the SWM4-NDP model? I wasn't making a declarative statement that it won't work. I was asking whether anyone had verified that using a massless Drude in that model actually reproduced all of the physical properties of the SWM4-NDP model. We do all of our development on the Drude FF with Drudes of mass = 0.4 amu and the extended Lagrangian. I don't know how a massless Drude behaves in this model. It may work fine, but you should very rigorously verify this yourself before doing anything by doing simulations of pure water. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 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] Problem with constraints in NVT calculations.
Dear all, I have been using the SWM4-NDP water model that works well with CHARMM27 force field. The force field (most recent version) was obtained from virtualchemistry, and consists of polarisable ions and the SWM4-NDP water model from Lamoureux et al.The water on graphene (energy minimisation and NVT) calculations are stable, and have produced a few NVT runs of up to 10ns.I also compared the NVT runs with other previously calculated structures, namely, the visualised NVT runs are very much comparable to that obtained by CHARMM27 force field with TIPS3P water model.However, as the polarisable H3O+ and Cl- ions are inserted into the simulation box, the NVT run tends to crash as a result of too many LINCS warnings.I suspect that the constraints in the H3O is the cause of the LINCS warnings, and after removing the [ constraints ] in the topology file, the calculation seems to be running.;[ constraints ];; i funct doh dhh;1 3 1 0.102;1 4 1 0.102;1 5 1 0.102;3 4 1 0.169124;4 5 1 0.169124;3 5 1 0.169124Can anyone please tell me if what I am doing is correct? As I am not sure if removing the H3O constraints in the NVT run is appropriate.With regard to the massless Drude and standard oxygen mass (thank you Justin for providing the information), I would like to know why are they not appropriate (as mentioned in the previous email) for the SWM4-NDP model?Thank you for taking the time to read this email. I would be more than happy to provide further details if needed.Regards,Kester -- 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.
