[gmx-users] Lincs warning spc

[dsh2002 at med.cornell.edu]

Hello all,
When I do an mdrun after about 100 steps, .2 picoseconds, in my
simulation I get an error that looks like this :

Step 100, time 0.2 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.003034 (between atoms 28321 and 28323) rms 0.000028
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  28321  28322   33.7    0.1002   0.1002      0.1000

I've narrowed down the problem possibly to this line in my mdp file:
define = -DFLEXIBLE ...

If I redo the run without defining -DFLEXIBLE, I can proceed without any
errors.
I have FLEXIBLE defined in the spc.itp to specify bond and angles for the
topology of spc as:

#ifdef FLEXIBLE
[ bonds ]
; i     j       funct   length  force.c.
1       2       1       0.1     345000  0.1     345000
1       3       1       0.1     345000  0.1     345000

[ angles ]
; i     j       k       funct   angle   force.c.
2       1       3       1       109.47  383     109.47  383
#else
[ settles ]
; OW    funct   doh     dhh
1       1       0.1     0.16333

[ exclusions ]
1       2       3
2       1       3
3       1       2
#endif


any ideas? Thanks once again, Danny.


copy of my mdp file:
cpp                 =  /lib/cpp
; define              =  -DFLEXIBLE   -DPOSRES_Protein  -DPOSRES_LIPID
-DPOSRES_WATER
integrator          =  md
dt                  =  0.002
nsteps              =  50000
nstcomm             =  1

;       Output control
nstxout             =  500.0
nstvout             =  500.0
nstlog              =  500.0
nstenergy           =  500.0
energygrps          =  PROTEIN          POPC            SOL_Cl

;       Neighbor searching
nstlist             =  10
ns_type             =  grid
pbc                 =  xyz

;       Electrostatics and VdW
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.2
fourierspacing      =  0.12
pme_order           =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes

;       Temperature coupling
Tcoupl              =  berendsen
tc_grps             =  PROTEIN          POPC            SOL_Cl
tau_t               =  0.1              0.1             0.1
ref_t               =  310              310             310

;       Pressure coupling
Pcoupl              =  berendsen
pcoupltype          =  semiisotropic
tau_p               =  5.0              5.0
compressibility     =  4.5e-5           4.5e-9
ref_p               =  1.0              1.0

;       Velocity generation
gen_vel             =  no
;gen_temp            =  310
;gen_seed            =  173529

;       Bonds
constraints         =  all-bonds
constraint_algorithm =  lincs
unconstrained_start =  no
lincs_order         =  4
lincs_iter          =  1
lincs_warnangle     =  30