Re: [gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you very much for your support. I am following Justin's tutorial but simulating a fragment of antibody (Fab). I will try the different water models. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 01:07 AM To: "gromacs.org_gmx-users"; Subject: Re: Re: Simulate protein at subzero condition in aqueous buffer Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Just one more thing. If you're following Justin's tutorial, I guess you're using lysozyme. This protein will not deviate very much from it's crystal structure at 27ºC, let alone at -40ºC (*in the context of a molecular dynamics simulation**). I understand that it may be possible to experimentally unfold this protein reversibly using low temperature and high pressure, but this may be unfeasible to perform using a regular protein force field and water model. It will not behave as you expect. * I should add that this is a very stable protein and the disulfide bonds (which cannot be broken during the simulation) make it almost impossible to unfold it completely at any temperature using molecular dynamics. /J On Wed, Jun 7, 2017 at 7:15 PM, João Henriques wrote: > Higher complexity water models such as TIP5P and so on are able to better > reproduce bulk water properties (please check the paper I linked in my > earlier email). However, these models require more computational effort > (due to the increased number of interactions) and may not work well in > conjunction with a protein (many protein force fields were developed to be > used with specific water models). As Justin said, none of them gets > everything right. > > /J > > On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote: > >> Dear Justin, >> Thank you very much. I will try the possible water models. >> >> >> Do you know if there are water models to resemble frozen state? >> >> >> Yours sincerely >> Cheng >> >> >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Thu, Jun 8, 2017 00:50 AM >> To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"> s.org_gmx-us...@maillist.sys.kth.se>; >> >> Subject: Re: Simulate protein at subzero condition in aqueous buffer >> >> >> >> Dear Joao, >> Thank you for your help and the paper link. >> >> >> I was following Justin's tutorial >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx >> -tutorials/lysozyme/03_solvate.html >> On that page, it says "spc216.gro as the solvent configuration for SPC, >> SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) >> after the solvation step. So I assume "spc216.gro" refer to all the >> three-point water models? >> >> >> I am trying to see if my protein will be denatured in cold condition. >> >> >> Yours sincerely >> Cheng >> >> >> -- Original -- >> From: "ZHANG Cheng";<272699...@qq.com>; >> Date: Wed, Jun 7, 2017 10:01 PM >> To: "gromacs.org_gmx-users"; >> Cc: "ZHANG Cheng"<272699...@qq.com>; >> Subject: Simulate protein at subzero condition in aqueous buffer >> >> >> >> Dear Gromacs, >> I would like to simulate the protein at subzero condition in aqueous >> buffer, to see if it becomes more stable than the elevated temperature >> (e.g. 65 C). Can I ask what is the valid temperature range for water >> "spc216.gro" ? If I run the simulation at -40 C, does it still assume the >> system as liquid state instead of frozen state? Thank you. >> >> >> Yours sincerely >> Cheng >> -- >> 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] Simulate protein at subzero condition in aqueous buffer
Higher complexity water models such as TIP5P and so on are able to better reproduce bulk water properties (please check the paper I linked in my earlier email). However, these models require more computational effort (due to the increased number of interactions) and may not work well in conjunction with a protein (many protein force fields were developed to be used with specific water models). As Justin said, none of them gets everything right. /J On Wed, Jun 7, 2017 at 7:07 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Justin, > Thank you very much. I will try the possible water models. > > > Do you know if there are water models to resemble frozen state? > > > Yours sincerely > Cheng > > > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Thu, Jun 8, 2017 00:50 AM > To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users" s.org_gmx-us...@maillist.sys.kth.se>; > > Subject: Re: Simulate protein at subzero condition in aqueous buffer > > > > Dear Joao, > Thank you for your help and the paper link. > > > I was following Justin's tutorial > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > gmx-tutorials/lysozyme/03_solvate.html > On that page, it says "spc216.gro as the solvent configuration for SPC, > SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) > after the solvation step. So I assume "spc216.gro" refer to all the > three-point water models? > > > I am trying to see if my protein will be denatured in cold condition. > > > Yours sincerely > Cheng > > > -- Original -- > From: "ZHANG Cheng";<272699...@qq.com>; > Date: Wed, Jun 7, 2017 10:01 PM > To: "gromacs.org_gmx-users"; > Cc: "ZHANG Cheng"<272699...@qq.com>; > Subject: Simulate protein at subzero condition in aqueous buffer > > > > Dear Gromacs, > I would like to simulate the protein at subzero condition in aqueous > buffer, to see if it becomes more stable than the elevated temperature > (e.g. 65 C). Can I ask what is the valid temperature range for water > "spc216.gro" ? If I run the simulation at -40 C, does it still assume the > system as liquid state instead of frozen state? Thank you. > > > Yours sincerely > Cheng > -- > 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] Simulate protein at subzero condition in aqueous buffer
Dear Justin, Thank you very much. I will try the possible water models. Do you know if there are water models to resemble frozen state? Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Thu, Jun 8, 2017 00:50 AM To: "ZHANG Cheng"<272699...@qq.com>; "gromacs.org_gmx-users"; Subject: Re: Simulate protein at subzero condition in aqueous buffer Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
On 6/7/17 12:50 PM, ZHANG Cheng wrote: Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? It is as Joao has said - that's just a coordinate file of a pre-equilibrated box of water that was generated using the SPC water model. You can indeed use it to simulate other 3-point water model systems following an initial equilibration. I am trying to see if my protein will be denatured in cold condition. The properties of the water model are going to be critical here. For instance, SPC has a maximum density around -41 C, which is obviously very unphysical (water has a real maximum density at +4 C) so if you're seeking to model behavior at -40 C, then SPC is a very bad choice because its properties are not realistic. I suggest you investigate the many possible water models that exist and find one or more that might reproduce some of the most important properties. None of them gets everything right. -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] Simulate protein at subzero condition in aqueous buffer
Dear Joao, Thank you for your help and the paper link. I was following Justin's tutorial http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/03_solvate.html On that page, it says "spc216.gro as the solvent configuration for SPC, SPC/E, or TIP3P water", and it outputs 10832 solvent molecules (i.e. water) after the solvation step. So I assume "spc216.gro" refer to all the three-point water models? I am trying to see if my protein will be denatured in cold condition. Yours sincerely Cheng -- Original -- From: "ZHANG Cheng";<272699...@qq.com>; Date: Wed, Jun 7, 2017 10:01 PM To: "gromacs.org_gmx-users"; Cc: "ZHANG Cheng"<272699...@qq.com>; Subject: Simulate protein at subzero condition in aqueous buffer Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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] Simulate protein at subzero condition in aqueous buffer
Hello, "spc216.gro" is not a water model, it's just a pre-equilibrated simulation box (300 K and 1 bar) with the coordinates of 216 3-site water molecules. SPC and TIP3P are two examples of 3-site water models. Water model properties are well studied and tabled (e.g. http://aip.scitation.org/doi/10.1063/1.1862245). I am no expert in pure water simulations, but I doubt 3-site water models can reproduce ice in a realistic way. Will the force field even hold at that temperature? I really don't understand why you'd want to try something like this. However, and to finish, there's one thing I can tell you for sure: your system will be much more "stable" at -40ºC. Why, because it will barely move from it's initial conformation, due to the very low thermal energy. In sum, you'll spend computational time sampling almost nothing. Best regards, João On Wed, Jun 7, 2017 at 4:01 PM, ZHANG Cheng <272699...@qq.com> wrote: > Dear Gromacs, > I would like to simulate the protein at subzero condition in aqueous > buffer, to see if it becomes more stable than the elevated temperature > (e.g. 65 C). Can I ask what is the valid temperature range for water > "spc216.gro" ? If I run the simulation at -40 C, does it still assume the > system as liquid state instead of frozen state? Thank you. > > > Yours sincerely > Cheng > -- > 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.
[gmx-users] Simulate protein at subzero condition in aqueous buffer
Dear Gromacs, I would like to simulate the protein at subzero condition in aqueous buffer, to see if it becomes more stable than the elevated temperature (e.g. 65 C). Can I ask what is the valid temperature range for water "spc216.gro" ? If I run the simulation at -40 C, does it still assume the system as liquid state instead of frozen state? Thank you. Yours sincerely Cheng -- 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.
