[gmx-users] g_wham error

[Justin A. Lemkul]

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
> 

-- 
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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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