Dear gmx users I am working on an umbrella sampling system.(lipid bilayer+drug). I have used distance here is my mdp file for pulling: title = Umbrella pulling simulation define = -DPOSRES_LIP ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 2500000 ; 5 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc_grps = DRG_DMPC SOL tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 5.0 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = LIPID pull_group1 = DRUG ;pull_init1 = 0 pull_rate1 = -0.1 pull_k1 = 500 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps
and also this is my umbrella mdp file: title = Umbrella pulling simulation define = -DPOSRES_LIP ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 500000 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 ; every 10 ps nstvout = 5000 nstfout = 500 nstxtcout = 500 ; every 1 ps nstenergy = 500 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = DRG_DMPC SOL tau_t = 0.5 0.5 ref_t = 310 310 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = LIPID pull_group1 = DRUG pull_init1 = 0 pull_rate1 = 0.0 pull_k1 = 1000 ; kJ mol^-1 nm^-2 pull_nstxout = 1000 ; every 2 ps pull_nstfout = 1000 ; every 2 ps I have used lipid as a refrence group and drug as a pull group.in npt_umbrella mdp I have used constraint for refrence group and in md_umbrella I have removed the constraint. After that my summery.dat file contains following data: 0 2.2163574 1 2.2125353 2 2.1688467 3 2.1041310 4 2.0907198 5 2.0372755 6 2.0344109 7 2.0205807 8 2.0188276 9 2.0063477 10 2.0100271 . . 495 1.6062210 496 1.5399962 497 1.5931936 498 1.6058899 499 1.6357416 500 1.5546903 I have applied 0,3,9,15,16,17,18,19,20,22,39,42 and 51 (from 0 to 500) points for my umbrella sampling. My questions: 1.why do I have only two peaks in my histogram curve? 2.I have seen in a paper using constraint for pull,to calculate delta G of system.I want to calcuate delta G of drug,what should I do?Any diffrence in using umbrella or constraint? 3.What is the best way in our system to calculate delta G? -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
