Scratch my post. I need to learn to read the manual more closely. I thought the PDO output was the distance and not the deviation from the restrained position.
Thanks, Ilya On Sat, Feb 23, 2008 at 1:04 PM, Ilya Chorny <[EMAIL PROTECTED]> wrote: > 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. > -- Ilya Chorny Ph.D.
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