[gmx-users] mdrun (nvt.mdp) wouldn't work

[MD]

Hi gromacs folks,

I was trying to do a mdrun using nvt.mdp and I got following error
messages. I am not quite sure what is causing the error and I am hoping to
get some help here. Is it because my starting structure is not good enough?
There were some broken residues but I had them fixed and the minimization
run was ok until the equilibration.

The command and notes  I had was as followed.


*  gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr*

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
Setting the LD random seed to 552293178
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Excluding 1 bonded neighbours molecule type 'NA'
turning all bonds into constraints...

NOTE 1 [file topol.top, line 53]:
  System has non-zero total charge: 0.140005
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.



Setting gen_seed to 2333002834
Velocities were taken from a Maxwell distribution at 300 K
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group Protein_MG_ATP is 11217.68
Number of degrees of freedom in T-Coupling group NA_SOL is 94242.32
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
Calculated rlist for 1x1 atom pair-list as 1.432 nm, buffer size 0.032 nm
Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 60x60x60, spacing 0.152 0.152 0.152
Estimate for the relative computational load of the PME mesh part: 0.08
This run will generate roughly 126 Mb of data

There was 1 note

Back Off! I just backed up nvt.tpr to ./#nvt.tpr.1#

gcq#207: "Is That a Real Poncho ?" (F. Zappa)



*gmx mdrun -deffnm nvt*


Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.004922, max 0.143141 (between atoms 4646 and 4648)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.

Step 0, time 0 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.018958, max 0.925037 (between atoms 4628 and 4630)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4608   4609   32.0    0.1016   0.1180      0.0997
   4608   4610   33.7    0.1555   0.2089      0.1430
  ...
Wrote pdb files with previous and current coordinates

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.015813, max 0.806353 (between atoms 4630 and 4631)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4608   4609   30.4    0.1180   0.1065      0.0997
   4608   4610   39.2    0.2089   0.1668      0.1430
  ...
Wrote pdb files with previous and current coordinates

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020826, max 0.666994 (between atoms 4628 and 4630)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4598   4606   42.2    0.1770   0.1820      0.1490
   4606   4607   48.7    0.1290   0.1290      0.1230
   ...
Wrote pdb files with previous and current coordinates

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3.113067, max 231.822983 (between atoms 4610 and 4611)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   4570   4571   42.8    0.1273   0.1912      0.1230
   4572   4573   87.4    0.1000   0.0886      0.0997
   4572   4574   54.9    0.1738   0.2588      0.1430
   ...
Wrote pdb files with previous and current coordinates

WARNING: Listed nonbonded interaction between particles 4606 and 4611
at distance 25.173 which is larger than the table limit 2.431 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.



Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 3736.447377, max 274785.437500 (between atoms 4598 and 4599)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    487    489   45.4    0.1345   0.1987      0.1345
    489    490   48.7    0.0997   0.1544      0.0997
    ...
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)

the nvt.mdp


title       = Protein-ligand complex NVT equilibration
define      = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 500       ; save coordinates every 1.0 ps
nstvout     = 500       ; save velocities every 1.0 ps
nstenergy   = 500       ; save energies every 1.0 ps
nstlog      = 500       ; update log file every 1.0 ps
energygrps  = Protein MG ATP
; Bond parameters
continuation    = no            ; 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_MG_ATP NA_SOL    ; 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      = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; 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