[gmx-users] Strange PDO output during umbrella sampling
Ilya Chorny
ichorny at gmail.com
Sat Feb 23 22:04:31 CET 2008
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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080223/4b189926/attachment.html>
More information about the gromacs.org_gmx-users
mailing list