[gmx-users] links warnangles

[vferrario at units.it]

Dear all,
I'm dealing with a simulation of a polymer in CHCL3, the polymer works  
good, but I have some problems with the CHCL3 definition in GROMOS  
53a6 ff.
I've taken the CHCL3 definition from the automated topology builder website:

http://compbio.biosci.uq.edu.au/atb/download.py?molid=1597&file=itp_uniatom

So the itp file of my CHCL3 definition is:

[ moleculetype ]
; Name            nrexcl
CLF             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass   
typeB    chargeB      massB
      1        CCL      1    CLF    CCl      1      0.179     12.011    
; qtot 0.179
      2        HCL      1    CLF    HCl      1      0.082      1.008    
; qtot 0.261
      3       CLCL      1    CLF    CL1      1     -0.087     35.453    
; qtot 0.174
      4       CLCL      1    CLF    CL2      1     -0.087     35.453    
; qtot 0.087
      5       CLCL      1    CLF    CL3      1     -0.087     35.453   ; qtot 0

[ constraints ]
     1     3     1     0.1758
     1     4     1     0.1758
     1     5     1     0.1758
     2     3     1     0.233839
     2     4     1     0.233839
     2     5     1     0.233839
     3     4     1     0.290283
     3     5     1     0.290283
     4     5     1     0.290283

I've generated a box of solvent, but when I try to minimize it with  
the following mdp file:

title		        = Minimization
cpp		        = /lib/cpp
include		        = -I../top
constraints             = none
integrator	        = steep
emtol		        = 2.5
emstep                  = 0.01
nsteps		        = 100000
nbfgscorr               = 10
nstenergy	        = 100
nstxtcout	        = 0
xtc_grps	        = system
energygrps	        = system
nstlist		        = 5
ns_type		        = grid
pbc                     = xyz
rlist		        = 1.0
coulombtype	        = cut-off
rcoulomb	        = 1.0
vdwtype                 = cut-off
rvdw		        = 1.4
fourierspacing	        = 0.15
fourier_nx              = 0
fourier_ny              = 0
fourier_nz              = 0
pme_order               = 4
optimize_fft            = yes
tcoupl                  = no
pcoupl                  = no
gen_vel                 = no
constraint_algorithm    = LINCS
lincs_order             = 8
lincs_iter              = 2
nstlog                  = 100
lincs_warnangle         = 90

The system crash giving me the following error:

Fatal error:
Too many LINCS warnings (1413)
If you know what you are doing you can adjust the lincs warning  
threshold in your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

My question is: why the system crash and why LINCS warnings are  
generated if all the molecule is constrained? What shell I do to avoid  
these probles? New CHCL3 definition?
Please help me, thank you in advance.

Valerio


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