lloyd riggs wrote:
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?
<snip>
integrator = md
dt = 0.005
With a timestep of 5 fs, you should (at minimum) be using constraints, and
probably virtual sites as well. Does a more sensible timestep (like 1 or 2 fs)
make your system stable?
nsteps = 1000
nstxout = 100000
nstvout = 100000
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_grps = system
energygrps = system
nstlist = 20
You should aim for an nstlist that will update your neighborlist roughly every
10-20 ps, or else (in theory) you could be missing interactions. With your
neighborlist updated every 100 ps (!) then your short-range interactions could
be changing quite a bit.
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
Coupling the whole system in one temperature bath may or may not be appropriate.
Although not the most likely culprit for your problem, you should be aware.
See here, particularly the cited references:
http://www.gromacs.org/Documentation/Terminology/Thermostats
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
In a periodic system, using this comm_mode is inappropriate. Surely grompp
warned you about this?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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