Re: [gmx-users] possible bug in posre
That means intercalation is affected directly by this, and the results will have no meaningful physical sense. Has anyone succssfully simulated intercalation in the DNA by some molecules without a method that disrupts the physicochemical energies of the DNA and the intercalator? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, August 30, 2017 4:50:55 PM Subject: Re: [gmx-users] possible bug in posre On 8/30/17 10:39 AM, Sergio Manzetti wrote: > Its only the constraints in DPOSRE that I am concerned about. They do keep > the antisense and the sense strands together, however, do they keep this > together so that also intercalation between the bases is not any longer > physically related? Constraints and restraints are different; -DPOSRES has nothing to do with constraints. Position restraints bias the positions of the affected atoms towards their reference coordinates. They are absolute in space, so they don't "keep strands together" in the literal sense, but they simply prevent/disfavor anything from moving. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
On 8/30/17 10:39 AM, Sergio Manzetti wrote: Its only the constraints in DPOSRE that I am concerned about. They do keep the antisense and the sense strands together, however, do they keep this together so that also intercalation between the bases is not any longer physically related? Constraints and restraints are different; -DPOSRES has nothing to do with constraints. Position restraints bias the positions of the affected atoms towards their reference coordinates. They are absolute in space, so they don't "keep strands together" in the literal sense, but they simply prevent/disfavor anything from moving. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
Its only the constraints in DPOSRE that I am concerned about. They do keep the antisense and the sense strands together, however, do they keep this together so that also intercalation between the bases is not any longer physically related? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, August 30, 2017 3:43:09 PM Subject: Re: [gmx-users] possible bug in posre On 8/30/17 9:33 AM, Sergio Manzetti wrote: > Weird stuff, because the 1 simulation turned out well, even without POSRE. > > Can this POSRE be reliable, in terms of intercalation of molecules? In other > words, does the energy that is imposed by POSRE really reflect the energy > landscape of the bonds simulated in the remaining of the molecules in the > box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the > DNA, then any intercalation study is really futile! You're talking about both constraints and restraints here, and typically restraints are applied to non-H atoms and constraints involve bonds to H atoms. Restraints are biasing potentials to prevent motion. You'll have to explain what you're studying and why you think you need restraints (which are typically only used during equilibration). Restraints are artificial, so anything that comes out of a restrained simulation should be interpreted with care, because you could be completely preventing relevant dynamics. Binding of a molecule to a restrained target may be completely unphysical. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
On 8/30/17 9:33 AM, Sergio Manzetti wrote: Weird stuff, because the 1 simulation turned out well, even without POSRE. Can this POSRE be reliable, in terms of intercalation of molecules? In other words, does the energy that is imposed by POSRE really reflect the energy landscape of the bonds simulated in the remaining of the molecules in the box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then any intercalation study is really futile! You're talking about both constraints and restraints here, and typically restraints are applied to non-H atoms and constraints involve bonds to H atoms. Restraints are biasing potentials to prevent motion. You'll have to explain what you're studying and why you think you need restraints (which are typically only used during equilibration). Restraints are artificial, so anything that comes out of a restrained simulation should be interpreted with care, because you could be completely preventing relevant dynamics. Binding of a molecule to a restrained target may be completely unphysical. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
Weird stuff, because the 1 simulation turned out well, even without POSRE. Can this POSRE be reliable, in terms of intercalation of molecules? In other words, does the energy that is imposed by POSRE really reflect the energy landscape of the bonds simulated in the remaining of the molecules in the box, by lincs? If the dposre is an aiddtional energy to the h-bonds of the DNA, then any intercalation study is really futile! Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "Justin Lemkul" <jalem...@vt.edu> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Wednesday, August 30, 2017 3:35:48 PM Subject: Re: [gmx-users] possible bug in posre On 8/30/17 9:21 AM, Sergio Manzetti wrote: > Hi, I have made 5 copies of a simulation, using the following mdp , with > gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is > a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is > bound to some other molecule and everything looks OK. In simulation 2, 3, 4 > and 5 the DNA strands fly everywhere in the box, outside the box and even > double up in longitude direction. All the directories are identical in their > files, and the grompp has been used respectively. Does this sound familiar to > some, or is it most likely a grompp error? This is the second time I try > this. > > > title = DNA in water stabilization > cpp = /lib/cpp > include = -I../top > define = The fact that there's no -DPOSRES here suggests you're probably not actually using restraints. Therefore, what you're seeing is your DNA diffusing across the box and experiencing the normal PBC imaging effects. If restraints are on, you'll see a corresponding energy term in the .log and .edr files. If it's not there, there are no restraints. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
On 8/30/17 9:21 AM, Sergio Manzetti wrote: Hi, I have made 5 copies of a simulation, using the following mdp , with gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the DNA strands fly everywhere in the box, outside the box and even double up in longitude direction. All the directories are identical in their files, and the grompp has been used respectively. Does this sound familiar to some, or is it most likely a grompp error? This is the second time I try this. title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = The fact that there's no -DPOSRES here suggests you're probably not actually using restraints. Therefore, what you're seeing is your DNA diffusing across the box and experiencing the normal PBC imaging effects. If restraints are on, you'll see a corresponding energy term in the .log and .edr files. If it's not there, there are no restraints. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] possible bug in posre
Hi, I have made 5 copies of a simulation, using the following mdp , with gen-seed = 17529, 17528, 17527, 17526 and 17525. In this simulation, thre is a piece of DNA; with posre etc. In simulation one, after 20 ns, the DNA is bound to some other molecule and everything looks OK. In simulation 2, 3, 4 and 5 the DNA strands fly everywhere in the box, outside the box and even double up in longitude direction. All the directories are identical in their files, and the grompp has been used respectively. Does this sound familiar to some, or is it most likely a grompp error? This is the second time I try this. title = DNA in water stabilization cpp = /lib/cpp include = -I../top define = integrator = md dt = 0.002 nsteps = 1000 nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 300 nstxout-compressed = 300 compressed-x-grps = PRB SOL NA CL DNA energygrps = PRB SOL NA CL DNA nstlist = 10 ns-type = grid rlist = 0.8 coulombtype = PME rcoulomb = 0.8 rvdw = 0.8 tcoupl = V-Rescale tc-grps = System tau-t = 0.1 ref-t = 310 Pcoupl = No tau-p = 1.0 compressibility = 4.5e-5 ref-p = 1.0 gen-vel = yes gen-temp = 310 gen-seed = 17529 constraints = all-bonds Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] -- 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.
