[gmx-users] Re: Change in the position of structural Zinc and calcium ions during MD
Hi Justin, Below I pasted .mdp file and topology. In .log file I could see energy term for position restraints. .mdp file--- title = NPT Equilibration define = -DPOSRES ; position restraints for protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 500 ; save velocities every 1 ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps ; Bond parameters continuation= yes ; 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 cels 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 = Nose-Hoover ; More accurate thermostat tc-grps = Protein_CA_ZN DMPC SOL_CL; three coupling groups - more accurate tau_t = 0.50.5 0.5 ; time constant, in ps ref_t = 298298 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL ; Scale COM of reference coordinates refcoord_scaling = com topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DMPC topology #include rama4LJ.ff/dmpcLJ.itp ; Include water topology #include rama4LJ.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include rama4LJ.ff/ions.itp ---.log file Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.59758e+042.74092e+04 -2.56846e+03 -4.68637e+05 -1.67418e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 7.09403e+02 -5.47088e+058.83115e+04 -4.58777e+053.07118e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.00493e+021.00080e+000.0e+00 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467p5012474.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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] Re: Change in the position of structural Zinc and calcium ions during MD
On 11/12/13 1:47 PM, Rama wrote: Hi Justin, Below I pasted .mdp file and topology. In .log file I could see energy term for position restraints. .mdp file--- title = NPT Equilibration define = -DPOSRES ; position restraints for protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 500 ; save velocities every 1 ps nstenergy = 500 ; save energies every 1 ps nstlog = 500 ; update log file every 1 ps ; Bond parameters continuation= yes ; 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 cels 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 = Nose-Hoover ; More accurate thermostat tc-grps = Protein_CA_ZN DMPC SOL_CL; three coupling groups - more accurate tau_t = 0.50.5 0.5 ; time constant, in ps ref_t = 298298 310 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5 ; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no; Velocity generation is off ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = Protein_DMPC SOL_CL ; Scale COM of reference coordinates refcoord_scaling = com topol.top ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Strong position restraints for InflateGRO #ifdef STRONG_POSRES #include strong_posre.itp #endif ; Include DMPC topology #include rama4LJ.ff/dmpcLJ.itp ; Include water topology #include rama4LJ.ff/spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include rama4LJ.ff/ions.itp Do you have appropriate [position_restraints] assigned in this topology? None of the above, as shown, pertains to the ions, and the only relevant #ifdef block that would be triggered by -DPOSRES is for the protein. -Justin ---.log file Energies (kJ/mol) AngleProper Dih. Ryckaert-Bell. Improper Dih. LJ-14 1.77761e+043.10548e+037.97673e+034.40586e+028.14131e+03 Coulomb-14LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. 2.59758e+042.74092e+04 -2.56846e+03 -4.68637e+05 -1.67418e+05 Position Rest. PotentialKinetic En. Total EnergyTemperature 7.09403e+02 -5.47088e+058.83115e+04 -4.58777e+053.07118e+02 Pres. DC (bar) Pressure (bar) Constr. rmsd -2.00493e+021.00080e+000.0e+00 Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Change-in-the-positon-of-structural-Zinc-and-calcium-ions-during-MD-tp5012467p5012474.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- == Justin A. Lemkul, Ph.D. 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 == -- gmx-users mailing
