[gmx-users] GROMACS 5 - problem with LINCS with freeze groups

[Tomek Wlodarski]

Hi,

I experience some strange behaviour and I wonder if this is a bug or I am
doing something wrong.
I am running test simulation to check freeze groups in new gromacs.
And I am getting LINCS Warnings for atoms which should be frozen...:

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 30 and 31)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     32     33   90.8    0.1010  23.4699      0.1010
     32     34   90.3    0.1010  71.2488      0.1010
[...]

my mdp file:

; RUN CONTROL PARAMETERS
integrator               = md
dt                       = 0.002   ; 2 femtosecond time step for integration
nsteps                   = 500000  ; 1ns

; OUTPUT CONTROL OPTIONS
nstxout              = 5000    ; save coordinates every 2 ps
nstvout              = 5000    ; save velocities every 2 ps
nstenergy             = 5000    ; save energies every 2 ps
nstlog           = 5000    ; update log file every 2 ps
energygrps           = Protein Non-Protein
nstxtcout                = 5000
xtc-grps                 = non-Water

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
cutoff-scheme            = group
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = pme
rcoulomb                 = 0.9
fourierspacing       = 0.12
ewald_rtol         = 1e-5
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
optimize_fft         = yes
vdw-type                 = Cut-off
rvdw                     = 1.2
energygrp_table         =

; Temperature coupling
Tcoupl                   = V-rescale
tc-grps                  = Protein    Non-Protein
tau_t                    = 0.1        0.1
ref_t                    = 300        300

; Freeze atoms
freezegrps               = Protein
freezedim                = Y Y Y
energygrp-excl           = Protein Protein

; Pressure coupling
pcoupl                   = no

;Velocity generation
gen_vel          = no
gen_temp         = 300
gen_seed         = -1

;Constrain all bonds
constraints         = all-bonds
constraint-algorithm     = Lincs
lincs_iter              = 2             ; accuracy of LINCS
lincs_order          = 6            ; also related to accuracy

Exactly the same system with the same mdp file I am running in Gromacs
4.6.5 and everything runs smoothly.
Any suggestions?
Thanks a lot!
Best

tomek