Hi,
I've gotten the following error with two of my simulation systems. Usually this
weird "variable ci" error means the system is unstable, and I've seen it before
when I've done a poor job of equilibrating. But now I'm seeing it a long time
into my simulations (after 48 ns in one case, 60 ns in the other). If I simply
re-submit the job, it runs fine. The error shown is as follows:
-------------------------------------------------------
Program mdrun_4.0_mpi, VERSION 4.0
Source code file: nsgrid.c, line: 357
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 180. It should have been within [ 0 .. 180 ]
-------------------------------------------------------
It seems to me that this "ci" variable is still within the range of 0->180, if
those values are inclusive.
My .mdp file is as follows:
title = NPT simulation for a membrane protein
; Run parameters
integrator = md
dt = 0.002
nsteps = 5000000 ; 10000 ps (10 ns)
tinit = 40000
nstcomm = 1
; Output parameters
nstxout = 50000 ; every 100 ps
nstvout = 50000
nstfout = 50000
nstlog = 5000 ; every 10 ps
nstenergy = 5000
nstxtcout = 5000
; Bond parameters
constraint_algorithm = lincs
constraints = all-bonds
continuation = yes
; Cut-off's and neighborsearching
nstlist = 5
ns_type = grid
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.2
; PME electrostatics parameters
coulombtype = PME
fourierspacing = 0.18
;fourier_nx = 0
;fourier_ny = 0
;fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
; Berendsen temperature coupling is on in three groups
Tcoupl = Nose-Hoover
tc_grps = Protein POPC SOL_NA+_CL-
tau_t = 0.1 0.1 0.1
ref_t = 310 310 310
; Pressure coupling is not on
Pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic
tau_p = 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
; Generate velocities is off
gen_vel = no
gen_temp = 310
gen_seed = 7041776
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr = EnerPres
Any ideas what's going on?
Thanks,
Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
