[gmx-users] Error while running protein-carbohydrate simulation

[Deep Bhattacharya]

Hello,
I am trying to simulate the system mentioned but its failing showing this
error message,
WARNING: Listed nonbonded interaction between particles 746 and 751
at distance 3f which is larger than the table limit 3f nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.



-------------------------------------------------------
Program mdrun, VERSION 4.6.5
Source code file: /util/src/gromacs/gromacs-4.6.5/src/mdlib/pme.c, line: 851

Fatal error:
1 particles communicated to PME node 13 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Jede der Scherben spiegelt das Licht" (Wir sind Helden)

Error on node 13, will try to stop all the nodes
Halting parallel program mdrun on CPU 13 out of 16

gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)

--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 13 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 13 with PID 117399 on
node c0323 exiting improperly. There are two reasons this could occur:

1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.

2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"

This may have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

Here is my .mdp file
title       = CD44 deHA_sulf_red complex MD simulation
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 5000000    ; 2 * 5000000 = 10000 ps (10 ns)
dt          = 0.002     ; 2 fs
; Output control
nstxout             = 50000         ; suppress .trr output
nstvout             = 50000         ; suppress .trr output
nstenergy           = 50000      ; save energies every 100.0 ps
nstlog              = 50000      ; update log file every 100.0 ps
compressed-x-grps   = System
energygrps          = Protein LIG
; Bond parameters
continuation    = yes           ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints     = all-bonds     ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter      = 1             ; accuracy of LINCS
lincs_order     = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type         = grid      ; search neighboring grid cells
nstlist         = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)
rvdw            = 1.4       ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype     = PME       ; Particle Mesh Ewald for long-range
electrostatics
pme_order       = 4         ; cubic interpolation
fourierspacing  = 0.16      ; grid spacing for FFT
; Temperature coupling
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein_LIG Water_and_ions    ; two coupling groups - more
accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
NPT
pcoupltype  = isotropic                     ; uniform scaling of box vectors
tau_p       = 2.0                           ; time constant, in ps
ref_p       = 1.0                           ; reference pressure, in bar
compressibility = 4.5e-5                    ; isothermal compressibility of
water, bar^-1
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no        ; assign velocities from Maxwell distribution

I have performed 100 ps NVT and NPT simulation before doing the MD run.
Please help





*Deep S Bhattacharya*

*Graduate Research Assistant*

Mohs Biomedical Imaging & Nanotechnology Group

Pharmaceutical Sciences

*University of Nebraska Medical Center*

4018 Eppley Science Hall  |  Omaha, NE 68198-6805

office 402.559.4349  | cell 402.906.1640

deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com