[gmx-users] Minimisation with frozen groups

reich at mpikg.mpg.de reich at mpikg.mpg.de
Thu Mar 27 16:23:52 CET 2008

Dear Gromacs-users,

I have been putting a protein and its hydration shell into the center of
an octahedral box and then been filling the remaining space with water
using genbox. I wanted to minimise the filled-in water, afterwards,
keeping the positions of the protein and the hydration shell fixed with

Performing the minimisation for several conformations of the protein and
its hydration shell one minimisation ended with the error message:

 t = 0.036 ps: Water molecule starting at atom 19012 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with
previous and current coordinates

In the minimisation of another conformation I received the error message:

Program mdrun, VERSION 3.3.1
Source code file: nsgrid.c, line: 226

Range checking error:[...]

Variable ci has value -2147483648. It should have been within [ 0 .. 294 ]
Please report this to the mailing list (gmx-users at gromacs.org)

I have chosen the following parameters for constraints and electrostratics:

constraints              = hbonds
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = no
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs-iter               = 4
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no

; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = Cut-off
; cut-off lengths
rvdw-switch              = 0
rvdw                     = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = No
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1
; Seperate tables between energy group pairs
energygrp_table          =
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = no

Does anyone know what went wrong?



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