[gmx-users] Re: Strange PDO output during umbrella sampling
Ilya Chorny
ichorny at gmail.com
Sat Feb 23 22:57:53 CET 2008
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 <ichorny at gmail.com> 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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