[gmx-users] Error : symtab get_symtab_handle 367 not found

[ARNAB MUKHERJEE]

Hi,

I am simulating a Martini coarse grained DNA protamine system. I have 1
infinite DNA + 1 protamine. Since while using the martini python script for
coarse graining it removes the 2 phosphate atoms of the terminal base
pairs, so in order to have the right infinite DNA system, while building
it, I had build 2 extra base pairs, which I removed them manually and
renumbered the topology .itp file atom numbers to match with the .gro file.
So my periodic cuboidal box size in Z direction (the DNA is aligned along
Z) is # of BPs*3.38 Angstrom, so that the pbc along Z makes the DNA
infinite.

The problem is when I simulate this system, during the short NPT
equilibration, it shows this error :

  Fatal error:
symtab get_symtab_handle 367 not found

The strange thing is if I submit a short run, in interactive mode for eg,
it runs fine, as long as it stays connected. But when I submit the complete
run in the cluster, it shows this error, before even starting Step 0. I
tried to google about this error, but didn't find much info. I have been
running this simulation in version 5.0.6. I checked also using newer
version of gromacs 5.1.4, it shows running status, but in the .log file it
shows this :

 Started mdrun on rank 0 Thu Jun 14 01:29:37 2018
           Step           Time         Lambda
              0        0.00000        0.00000


Not all bonded interactions have been properly assigned to the domain
decomposition cells

Are the 2 different errors that I get in the different versions, connected?

To test if there is a problem in the force field (.itp file) since I had to
modify it manually to renumber the atoms, I ran a finite 50 BP DNA with
modified .itp file for the 50 BP DNA, and it runs fine.

I am not able to understand what is the problem. I am pasting my input .mdp
parameters that I used for the run. I used semiisotropic pressure coupling
as I want to keep the Z dimension of the box constant. I have also frozen 4
atoms in the 2 ends of the DNA since I want to keep the DNA aligned along
Z, since I later want to apply an E field along Z direction.

 title       = NVT equilibration with position restraint on all solute
(topology modified)
; Run parameters
integrator  = md        ; leap-frog integrator
;nsteps     = 30000000  ; 1 * 500000 = 500 ps
nsteps      = 500000
dt          = 0.001     ; 1 fs
; Output control
nstxout     = 0 ; save coordinates every 10 ps
nstvout     = 0 ; save velocities every 10 ps
nstcalcenergy   = 50
nstenergy   = 1000  ; save energies every 1 ps
nstxtcout       = 2500
;nstxout-compressed  = 5000   ; save compressed coordinates every 1.0 ps
                             ; nstxout-compressed replaces nstxtcout
;compressed-x-grps  = System  ; replaces xtc-grps
nstlog      = 1000  ; update log file every 1 ps
; Bond parameters
continuation    = no   ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none          ; all bonds (even heavy atom-H bonds)
constrained
;lincs_iter = 2                 ; accuracy of LINCS
lincs_order = 4                 ; also related to accuracy
epsilon_r       = 15
; Neighborsearching
cutoff-scheme   = Verlet
ns_type     = grid      ; search neighboring grid cels
nstlist     = 10            ; 20 fs
rvdw_switch     = 1.0
rlist       = 1.2       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.2       ; short-range electrostatic cutoff (in nm)
rvdw        = 1.2       ; short-range van der Waals cutoff (in nm)
vdwtype         = Cut-off       ; Twin range cut-offs rvdw >= rlist
;vdw-modifier    = Force-switch
;Electrostatics
coulombtype = PME       ; Particle Mesh Ewald for long-range electrostatics
pme_order   = 4         ; cubic interpolation
fourierspacing  = 0.12      ; grid spacing for FFT
; Temperature coupling is on
tcoupl          = v-rescale
tc_grps         = System
tau_t           = 1.0
ref_t           = 300

;energygrps = DNA W_ION_Protein
;energygrp-excl = DNA DNA
freezegrps = DNA-Frozen-Atoms
freezedim = Y Y Y

; Pressure coupling is off
;pcoupl     = no        ; no pressure coupling in NVT
Pcoupl     = parrinello-rahman
Pcoupltype  = semiisotropic
tau_p       = 5.0
compressibility = 3e-4 0
ref_p       = 1.0 1.0
; Periodic boundary conditions
pbc     = xyz       ; 3-D PBC
; Dispersion correctiion
DispCorr    = no        ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the
solvent/ions
nstcomm     = 50
comm-mode   = Linear
comm-grps       = System
;
refcoord_scaling = com
;refcoord_scaling = all

I would highly appreciate any help.

Thank you in advance,

Regards,

Arnab Mukherjee