[gmx-users] problem of GB simulation

[Vytautas Rakeviius]

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:  
 
 Hello,

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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