[gmx-users] strange lincs warning with version 4.6

[sebastian]

Dear GROMCS user,

I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on my 
local desktop (2*GTX 670 + i7) and everything works as smooth as 
possible. The outcomes are very reasonable and match the outcome of the 
4.5.5 version without GPU acceleration. On our cluster (M2090+2*Xeon 
X5650) I installed the  VERSION 4.6-dev-20121120-0290409. Using the same 
.tpr file used for runs with my desktop I get lincs warnings that the 
watermolecules can't be settled.
My .mdp file looks like:

  ;
title        = ttt
cpp                 =  /lib/cpp
include             = -I../top
constraints         =  hbonds
integrator          =  md
cutoff-scheme       =  verlet

;define              =  -DPOSRES            ; for possition restraints

dt                  =  0.002            ; ps !
nsteps              =  100000000              \
nstcomm             =  25            ; frequency for center of mass 
motion removal
nstcalcenergy       =  25
nstxout             =  100000            ; frequency for writting the 
trajectory
nstvout             =  100000            ; frequency for writting the 
velocity
nstfout             =  100000            ; frequency to write forces to 
output trajectory
nstlog              =  10000            ; frequency to write the log file
nstenergy           =  10000            ; frequency to write energies to 
energy file
nstxtcout           =  10000

xtc_grps            =  System

nstlist             =  25            ; Frequency to update the neighbor list
ns_type             =  grid            ; Make a grid in the box and only 
check atoms in neighboring grid cells when constructing a new neighbor
rlist               =  1.4            ; cut-off distance for the 
short-range neighbor list

coulombtype         =  PME            ; Fast Particle-Mesh Ewald 
electrostatics
rcoulomb            =  1.4            ; cut-off distance for the coulomb 
field
vdwtype             =  cut-off
rvdw                =  1.4            ; cut-off distance for the vdw field
fourierspacing      =  0.12            ; The maximum grid spacing for 
the FFT grid
pme_order           =  6            ; Interpolation order for PME
optimize_fft        =  yes
pbc            =  xyz
Tcoupl              =  v-rescale
tc-grps             =  System
tau_t               =  0.1
ref_t               =  300

energygrps          =  Protein Non-Protein

Pcoupl              =  no;berendsen
tau_p               =  0.1
compressibility     =  4.5e-5
ref_p               =  1.0
nstpcouple        =  5
refcoord_scaling    =  all
Pcoupltype          =  isotropic
gen_vel             =  no;yes
gen_temp            =  300
gen_seed            =  -1


Thanks a lot

Sebastian