[gmx-users] RE:Range checking error

[lloyd riggs]

Dear All,

Before I start, I have already searched through the mailing list archives, etc...and have energy minimized my structure (s) ;

I get the range check error;
_________________________________________________________________________
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might end up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.

Variable ci has value -2147483648. It should have been within [ 0 .. 19683 ]
__________________________________________________________________________

does anyone have a fix for this?  

I have first energy minimized my structures.  There are two seperate proteins with two seperate protein domains (chain a,b each) making up two receptors which interact with eachother transiently, or strongly in the presence of a molecule.  The two proteins are seperated (manually) by 10 angstroms.

I first energy minimized these, then added waters and ions.  I had problems with force fields that recognized all the ions (Mg2+, Ca2+, K+, Na+, Cl-) and ended up using the oplsaa force fields.

Now, I try an initial run, MD or a simple 100 step energy minimization, prior to a long run, and get the above error again and again.  The two scripts mentioned are below inline.  I have however played around with everything I could.  I have also started from scratch 3 times, ie the initial proteins-minimize-add waters/ions-and then it crashes?

Also, does anyone know what the variable "ci" is?  

Thanks for any help

Stephan Watkins
____________________________________________________________
Energy minimize short;

title               =  
cpp                 = 
define              =
constraints         =  none
integrator          =  steep
tinit               =  0
dt                  =  0.002    ; ps !
nsteps              =  100
init_step           =  0

;
;       Energy minimizing stuff
;
emtol               =  100.0
emstep              =  0.02
______________________________________________________________
energy minimize long;


constraints         =  all-bonds
integrator          =  cg
dt                  =  0.002    ; ps !
nsteps              =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
 ;
 ;       Energy minimizing stuff
 ;
 emtol               =  1000.0
 emstep              =  0.01
nstcgsteep          =  25
__________________________________________________
and  the MD run file;

 
integrator = md 
dt = 0.005 
nsteps = 1000 
nstxout = 100000 
nstvout = 100000 
nstlog = 1000 
nstenergy = 1000 
nstxtcout = 1000 
xtc_grps = system 
energygrps = system 
nstlist = 20 
coulombtype = PME 
ns_type = grid 
rlist = 1.5 
rcoulomb = 1.5 
rvdw = 1.5 
pbc = xyz 
table-extension = 20

;Temperature coupling 
tcoupl  = berendsen
tc-grps = system 
tau_t = 1.0
ref_t = 50.0 

; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          =  isotropic
tau_p               =  2.01
compressibility     =  4.5e-5
ref_p               =  1.0
refcoord_scaling    =  all

;Velocity generation 
gen_vel = yes 
gen_temp = 50.0 
gen_seed = 30 
ld_seed = 130 
comm_mode = angular 

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