[gmx-users] problem of GB simulation
vytautas1987 at yahoo.com
Thu Oct 5 12:29:03 CEST 2017
Most likely you do something wrong in energy minimization step:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.htmlMake sure you produce plot similar like in that page with your system before proceeding further with minimized system.
On Wednesday, October 4, 2017, 9:18:48 PM GMT+3, Albert <mailmd2011 at gmail.com> wrote:
I am using the following .mdp file for protein BG solvent simulations.
However, the job always failed with the following messages:
vol -0.00! imb F 22% step 144100, remaining wall clock time: 207 s
vol -0.00! imb F 23% step 144200, remaining wall clock time: 207 s
vol -0.00! imb F 23% step 144300, remaining wall clock time: 207 s
vol -0.00! imb F 23% step 144400, remaining wall clock time: 207 s
Program gmx mdrun, VERSION 5.1.4
Source code file:
/icm/home/albert/tmp/gromacs-5.1.4/src/gromacs/mdlib/nsgrid.c, line: 633
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 ind has value 131. It should have been within [ 0 .. 131 ]
The initial system seems to be all right since it is a liner peptide.
The initial energy of the peptide is also very low. I am not so sure
whether my .mdp is correct or not....
Thank you very much.
define = -DREST_ON -DSTEP_NVT
integrator = md
dt = 0.001
nsteps = 300000
nstlog = 1000
implicit_solvent = GBSA
gb_algorithm = OBC
;nstgbradii = 1.0
rgbradii = 1.0
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm = ace-approximation
sa_surface_tension = 0.0054
pbc = no
coulombtype = cut-off
cutoff-scheme = group
nstlist = 20
rlist = 1.0
tcoupl = Nose-Hoover
tc_grps = Protein
tau_t = 1.0
ref_t = 310
constraints = h-bonds
constraint_algorithm = LINCS
nstcomm = 100
comm_mode = angular
comm_grps = Protein
gen-vel = yes
gen-temp = 310
gen-seed = -1
refcoord_scaling = com
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