Hi All, I am trying to do umbrella sampling and I am getting very strange PDO output. The PDO out put does not correspond to the distances between groups. Below is my pdo output my mdp and ppa info and log file info showing the distances. I compared the values with output from g_dist just to verify. I also tried these run using 3.3.1(windows) and 3.3.2(unix) and got the same results. Any ideas?
Thanks, Ilya LOG: REFERENCE TYPE: center of mass of reference group Looking for group AMM1: found group AMM1: 5 elements. First: 110535 Looking for group AMM2: found group AMM2: 5 elements. First: 110540 Looking for group AMM3: found group AMM3: 5 elements. First: 110545 Looking for group Backbone: found group Backbone: 3159 elements. First: 1 Initializing pull groups. Inv. mass of group 1: 0.055436 Initial coordinates center of mass: 4.051 5.855 5.049 Initializing pull groups. Inv. mass of group 2: 0.055436 Initial coordinates center of mass: 6.770 5.254 5.102 Initializing pull groups. Inv. mass of group 3: 0.055436 Initial coordinates center of mass: 5.992 8.042 5.153 Initializing reference group. Inv. mass: 0.000025 Initial coordinates center of mass: 5.768 6.669 5.128 Initial distance of group 1: 0.079 Initial distance of group 2: 0.026 Initial distance of group 3: 0.025 PDO: # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 10 # Ref. Group 'Backbone' # Nr. of pull groups 3 # Group 1 'AMM1' Umb. Pos. 1.000000 Umb. Cons. 3000.000000 # Group 2 'AMM2' Umb. Pos. 1.000000 Umb. Cons. 3000.000000 # Group 3 'AMM3' Umb. Pos. 1.000000 Umb. Cons. 3000.000000 ##### 0.000000 -1.079179 -1.025911 -0.974844 0.020000 -1.044042 -0.982954 -0.939136 0.040000 -0.958650 -0.880464 -0.881684 0.060000 -0.900585 -0.736330 -0.794391 0.080000 -0.836541 -0.572538 -0.687577 0.100000 -0.747026 -0.457461 -0.573687 0.120000 -0.643660 -0.390060 -0.541646 0.140000 -0.616448 -0.321599 -0.549098 0.160000 -0.563586 -0.251571 -0.546965 0.180000 -0.491574 -0.176946 -0.526960 0.200000 -0.474667 -0.097256 -0.487377 MDP: ; VARIOUS PREPROCESSING OPTIONS title = ; Preprocessor - specify a full path if necessary. cpp = \\winsc\mvs8\VC\bin\AMD64\CL /EP include = define = ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0 dt = .002 nsteps = 100 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 10 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.2 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.2 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdwtype = switch ; cut-off lengths rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure dispcorr = EnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = nose-hoover ; Groups to couple separately tc-grps = System ; Time constant (ps) and reference temperature (K) tau-t = 1.0 ref_t = 298 ; Pressure coupling pcoupl = Parrinello-Rahman Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.01 1.01 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = yes gen-temp = 298 gen-seed = -1 ; OPTIONS FOR BONDS constraints = all-bonds PPA: ; ; File 'NeRh50_PMF_0.04.ppa' was generated ; By user: onbekend (0) ; On host: onbekend ; At date: Tue Jan 29 21:18:47 2008 ; ; GENERAL verbose = no Skip steps = 10 ; Runtype: afm, constraint, umbrella runtype = umbrella ; Number of pull groups ngroups = 3 ; Groups to be pulled group_1 = AMM1 group_2 = AMM2 group_3 = AMM3 ; The group for the reaction force. reference_group = Backbone ; Weights for all atoms in each group (default all 1) weights_1 = weights_2 = weights_3 = reference_weights = ; Ref. type: com, com_t0, dynamic, dynamic_t0 reftype = com ; Use running average for reflag steps for com calculation reflag = 1 ; Select components for the pull vector. default: Y Y Y pulldim = N N Y ; DYNAMIC REFERENCE GROUP OPTIONS ; Cylinder radius for dynamic reaction force groups (nm) r = 0 ; Switch from r to rc in case of dynamic reaction force rc = 0 ; Update frequency for dynamic reference groups (steps) update = 1 ; CONSTRAINT RUN OPTIONS ; Direction, default: 0 0 0, no direction constraint_direction = 0.0 0.0 0.0 ; Constraint distance (nm), default: 0, use starting distance constraint_distance1 = 0 constraint_distance2 = 0 constraint_distance3 = 0 ; Rate of chance of the constraint length, in nm/ps constraint_rate1 = 0 constraint_rate2 = 0 constraint_rate3 = 0 ; Tolerance of constraints, in nm constraint_tolerance = 1e-06 ; AFM OPTIONS ; Pull rates in nm/ps afm_rate1 = .000 afm_rate2 = .000 afm_rate3 = .000 ; Force constants in kJ/(mol*nm^2) afm_k1 = 0.0 afm_k2 = 0.0 afm_k3 = 0.0 ; Directions afm_dir1 = 0.0 0.0 0.0 afm_dir2 = 0.0 0.0 0.0 afm_dir3 = 0.0 0.0 0.0 ; Initial spring positions afm_init1 = 0.0 0.0 0.0 afm_init2 = 0.0 0.0 0.0 afm_init3 = 0.0 0.0 0.0 ; UMBRELLA SAMPLING OPTIONS ; Force constants for umbrella sampling in kJ/(mol*nm^2) ; Centers of umbrella potentials with respect to reference: ; Ref - Pull. k1 = 3000 pos1 = 0.0 0.0 1.0 K2 = 3000 pos2 = 0.0 0.0 1.0 K3 = 3000 pos3 = 0.0 0.0 1.0 -- Ilya Chorny Ph.D.
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