Re: [gmx-users] simmulated annealing excess temperature........................
On Thu, Aug 16, 2012 at 1:57 PM, tarak karmakar tarak20...@gmail.com wrote: Dear All, In my simulation I want the temperature of the system to be reached at 300 K only after 3 ps. But after 3ps I see temperature became 402 K. So am I doing any mistake in the '.mdp' file given below? ;temperature coupling is on Tcoupl = berendsen tau_t = 0.01 tc_grps = system ref_t = 0 Your tau_t seems too short. A value of 0.5 to 1 ps is normally recommended and used in publications such as [1]. I'm not sure how realistic such short tau_t is. Also, I'm not sure if a more standard tau_t would behave with such short allealing cycles. Is tehre any special reason to use this short cycle istead of an usual velocity generation (gen_vel)? [1] Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa and David van der Spoel Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant, J. Chem. Theor. Comput., 8, 61-74 (2012) doi: 10.1021/ct200731v -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] simmulated annealing excess temperature........................
Dear All, In my simulation I want the temperature of the system to be reached at 300 K only after 3 ps. But after 3ps I see temperature became 402 K. So am I doing any mistake in the '.mdp' file given below? define= -DFLEXIBLE constraints= h-bonds integrator = sd dt= 0.001 ; 1fs nsteps = 3000 ; 3ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog= 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype= cut-off coulombtype= cut-off pbc= no table-extension = 20.0 nstlist= 100 ns_type= grid rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 comm-mode = angular comm-grps= system optimize_fft= yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 3 annealing_temp = 0 300 ld_seed = 8072012 ;temperature coupling is on Tcoupl = berendsen tau_t = 0.01 tc_grps = system ref_t = 0 ;Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 Thanks, -- Tarak -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simmulated annealing excess temperature........................
On 8/16/12 12:57 PM, tarak karmakar wrote: Dear All, In my simulation I want the temperature of the system to be reached at 300 K only after 3 ps. But after 3ps I see temperature became 402 K. So am I doing any mistake in the '.mdp' file given below? You have a few. 1. You should not run MD with flexible water. 2. Finite cutoffs lead to rounding errors and accumulation of heat. This is most likely the source of your problem. I seem to recall Mark (or maybe someone else) already told you about this point. -Justin define= -DFLEXIBLE constraints= h-bonds integrator = sd dt= 0.001 ; 1fs nsteps = 3000 ; 3ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog= 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype= cut-off coulombtype= cut-off pbc= no table-extension = 20.0 nstlist= 100 ns_type= grid rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 comm-mode = angular comm-grps= system optimize_fft= yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 3 annealing_temp = 0 300 ld_seed = 8072012 ;temperature coupling is on Tcoupl = berendsen tau_t = 0.01 tc_grps = system ref_t = 0 ;Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 Thanks, -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simmulated annealing excess temperature........................
Thanks a lot for the quick reply...probably I have overlooked this point earlier ..now I'm getting it properly On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/16/12 12:57 PM, tarak karmakar wrote: Dear All, In my simulation I want the temperature of the system to be reached at 300 K only after 3 ps. But after 3ps I see temperature became 402 K. So am I doing any mistake in the '.mdp' file given below? You have a few. 1. You should not run MD with flexible water. 2. Finite cutoffs lead to rounding errors and accumulation of heat. This is most likely the source of your problem. I seem to recall Mark (or maybe someone else) already told you about this point. -Justin define= -DFLEXIBLE constraints= h-bonds integrator = sd dt= 0.001 ; 1fs nsteps = 3000 ; 3ps nstcomm = 1 nstxout = 1000 ; frequency to write coordinates to output trajectory nstvout = 0 ; frequency to write velocities to output trajectory; the last velocities are always written nstfout = 0 ; frequency to write forces to output trajectory nstlog= 10 ; frequency to write energies to log file nstenergy = 100 ; frequency to write energies to edr file nstcalcenergy = 100 vdwtype= cut-off coulombtype= cut-off pbc= no table-extension = 20.0 nstlist= 100 ns_type= grid rlist= 1.0 rcoulomb = 1.2 rvdw = 1.2 comm-mode = angular comm-grps= system optimize_fft= yes ;heating annealing = single annealing_npoints = 2 annealing_time = 0 3 annealing_temp = 0 300 ld_seed = 8072012 ;temperature coupling is on Tcoupl = berendsen tau_t = 0.01 tc_grps = system ref_t = 0 ;Pressure coupling is off Pcoupl = no ; Generate velocites is on gen_vel = yes gen_temp = 0 gen_seed = 8042012 Thanks, -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
