Gard Nelson wrote:
Hi all,
I'm trying to analyze a series of umbrella sampling windows, but I get
the following error:
Program g_wham, VERSION 4.0.7
Source code file: gmx_wham.c, line: 1397
Fatal error:
Found 1 pull groups in onePREP0.tpr,
but 1 data columns in onePREP0.xvg (expected 6)
my .mdp file is:
title = 1ns prep run, 0.0 A distance
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 * 500000 = 1ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; Velocity generation is on
; COM Pulling
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y; or N N N
pull_start = yes
pull_nstxout = 1000
pull_nstfout = 1000
pull_ngroups = 1
pull_group0 = COM
pull_weights0 =
pull_pbcatom0 = 0
pull_group1 = MYR-C
pull_weights1 =
pull_init1 = 0.00
pull_k1 = 5000
Where could this error be coming from?
Somewhere in the .xvg file. Can you post the first few actual data lines of the
file that g_wham is complaining about? As well, what command did you use to
execute g_wham? Is onePREP0.xvg a pullf or pullx output file?
-Justin
Thanks,
Gard
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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