Re: [gmx-users] MD simullations with Morse potential
Hi Justin, Thanks very much for your reply! Regarding to your two explanations, I guess it might be the first one. I have also tried to do a simulation of a three-residue (Gly-Ser-Asn) system with water, but it still did not work. Could you also give some test for this morse potential? Thanks very much! All the best, Qinghua On 04/26/2014 12:31 AM, Justin Lemkul [via GROMACS] wrote: On 4/25/14, 5:37 PM, fantasticqhl wrote: Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much! Well, Morse potentials aren't the functional form with which any of the biomolecular force fields in Gromacs were parametrized, so either (1) there's a bug that needs to be fixed or (2) you're doing something incompatible and the model physics is breaking down. -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 [hidden email] /user/SendEmail.jtp?type=nodenode=5016073i=0 | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul http://mackerell.umaryland.edu/%7Ejalemkul == -- 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 [hidden email] /user/SendEmail.jtp?type=nodenode=5016073i=1. If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016073.html To unsubscribe from MD simullations with Morse potential, click here http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5016062code=ZmFudGFzdGljcWhsQGdtYWlsLmNvbXw1MDE2MDYyfDE5NzE0ODU3Nzc=. NAML http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016087.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MD simullations with Morse potential
Hi Tsjerk, Thanks! Is morse potential working for you? I am using Gromos 53a6 force field with spc water, and the Gromacs version is 4.5.4, and I also tried 4.6.5. I just tried to do a simulation for just one residue (Gly) with water. However, all tests were not working! Could you tell me how you did the equilibrations? Thanks very much! All the best, Qinghua On 04/27/2014 11:30 AM, Tsjerk Wassenaar [via GROMACS] wrote: Hi Qinghua, I have run simulations with morse bonds a while back, in combination with the Gromos 45a3 force field. I only had a few of those bonds, though. Which Gromacs version are you using and which force field? Cheers, Tsjerk On Apr 27, 2014 10:44 AM, fantasticqhl [hidden email] /user/SendEmail.jtp?type=nodenode=5016089i=0 wrote: -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016090.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MD simullations with Morse potential
Dear All, I am trying to do a simulations with morse potential for bonds, I can do the minimization of the system, but I can not do the MD optimization without lincs constraints on bonds since using Morse potential with constraints is useless. The error was shown as Segmentation fault (core dumped) , I did not found some other information in the log file. The system was well minimized before doing md optimization. Here is my mdp file: ## title = OPLS Lysozyme NPT equilibration ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 10; 2 * 5 = 100 ps dt = 0.0005; 2 fs ; Output control nstxout = 2500; save coordinates every 0.2 ps nstvout= 2500; save velocities every 0.2 ps nstenergy= 2500 ; save energies every 0.2 ps nstlog = 2500 ; update log file every 0.2 ps ; Bond parameters continuation= no ; Restarting after NVT ;constraint_algorithm = lincs ; holonomic constraints ;constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter= 1 ; accuracy of LINCS ;lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel= yes ; Velocity generation is off gen_temp= 300 ; temperature for Maxwell distribution gen_seed= 173529 ; generate a random seed morse = yes Is there some special rule for md simulations with morse potential? But I did not found it in the manual. Could someone give some suggestions? Any response will be highly appreciated! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MD simullations with Morse potential
On 4/25/14, 10:00 AM, fantasticqhl wrote: Dear All, I am trying to do a simulations with morse potential for bonds, I can do the minimization of the system, but I can not do the MD optimization without lincs constraints on bonds since using Morse potential with constraints is useless. The error was shown as Segmentation fault (core dumped) , I did not found some other information in the log file. The system was well minimized before doing md optimization. Here is my mdp file: ## title = OPLS Lysozyme NPT equilibration ;define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 10; 2 * 5 = 100 ps dt = 0.0005; 2 fs ; Output control nstxout = 2500; save coordinates every 0.2 ps nstvout= 2500; save velocities every 0.2 ps nstenergy= 2500 ; save energies every 0.2 ps nstlog = 2500 ; update log file every 0.2 ps ; Bond parameters continuation= no ; Restarting after NVT ;constraint_algorithm = lincs ; holonomic constraints ;constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained ;lincs_iter= 1 ; accuracy of LINCS ;lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist= 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t= 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p= 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel= yes ; Velocity generation is off gen_temp= 300 ; temperature for Maxwell distribution gen_seed= 173529 ; generate a random seed morse = yes Is there some special rule for md simulations with morse potential? But I did not found it in the manual. Could someone give some suggestions? Any response will be highly appreciated! The first problem I suspect is the use of the Parrinello-Rahman barostat while generating velocities. That combination often results in instability for any system. Try NVT equilibration before moving to NPT. -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] MD simullations with Morse potential
Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/MD-simullations-with-Morse-potential-tp5016062p5016072.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] MD simullations with Morse potential
On 4/25/14, 5:37 PM, fantasticqhl wrote: Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much! Well, Morse potentials aren't the functional form with which any of the biomolecular force fields in Gromacs were parametrized, so either (1) there's a bug that needs to be fixed or (2) you're doing something incompatible and the model physics is breaking down. -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] MD simullations with Morse potential
Hi Qinghua, Can you run NVT equilibration? Does it work with nstlist set to 1? Cheers, Tsjerk On Apr 26, 2014 12:29 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/25/14, 5:37 PM, fantasticqhl wrote: Dear Justin, Thanks very much for your reply! I guess the use of the Parrinello-Rahman barostat should not be a problem because the optimization ran successfully if I turned off the morse potential. Actually, I have already done the nvt optimization without morse potential before I moved to npt optimization with morse potential, the error was the same for nvt with morse potential. I just do not know why the morse potential was not working. Do you have some other ideas which may result in the problem? Thanks very much! Well, Morse potentials aren't the functional form with which any of the biomolecular force fields in Gromacs were parametrized, so either (1) there's a bug that needs to be fixed or (2) you're doing something incompatible and the model physics is breaking down. -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. -- 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.
