[gmx-users] Error during npt equilibration in coarse grained simulation

[Anu Chandran]

Dear users,
I am trying to do a coarse grained simulation of an octamer of a 350
residue protein in water using gromacs-4.5.3 using martini force field. I
got the following error when i started running NPT equilibration

"Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 16.561310, max 137.568573 (between atoms 626 and 627)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 438.087891, max 3717.233887 (between atoms 580 and 581)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    626    627  121.9    0.2705  36.7207      0.2650
    621    622   90.0    0.2756   0.4600      0.2700
    624    626   91.5    0.3368 269.7515      0.3300
    621    623   90.0    0.2756   0.3172      0.2700
    620    624   90.4    0.3164 432.6003      0.3100
    622    623   90.0    0.2756   0.3991      0.2700
    618    620   85.5    0.3164 477.1006      0.3100
    626    627  121.9    0.2705  36.7206      0.2650
    615    618   88.6    0.3164 211.2461      0.3100
    607    610  141.3    0.3164  14.3253      0.3100

Step 32, time 0.64 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 134.347206, max 2000.691284 (between atoms 4949 and 4946)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    610    612  149.2    0.3164  17.6610      0.3100
    612    614   89.7    0.3164   3.1394      0.3100
    614    615  150.9    0.3164   9.9306      0.3100
    615    618   88.6    0.3164 211.1131      0.3100
    618    620   85.5    0.3164 477.0737      0.3100
    620    624   90.4    0.3164 432.5994      0.3100
   4950   4949   75.8    0.3164 146.5132      0.3100
    624    626   91.5    0.3368 269.7514      0.3300
   4952   4950  118.9    0.3164  14.6303      0.3100
    468    469   90.0    0.2705  24.6834      0.2650
   4941   4939   90.0    0.3368   8.5601      0.3300
    585    586   61.3    0.2756   0.3361      0.2700
   4944   4941   82.5    0.3164 206.9830      0.3100
    586    587   90.1    0.2756   0.3137      0.2700
   4946   4944   90.0    0.3164 583.5660      0.3100
    606    607   90.0    0.3368   6.6314      0.3300
   4949   4946   90.0    0.3164 620.5243      0.3100
    580    581   91.9    0.4030 1003.9232      0.2700
   4954   4952   90.3    0.3164   1.6571      0.3100
    580    582   89.8    0.2756 960.9988      0.2700
    582    583   98.6    0.2756 592.0677      0.2700
    463    464   90.0    0.2654   7.6858      0.2600
    581    582   88.8    0.1280 193.0707      0.2700
    581    583   91.3    0.2254 514.1149      0.2700
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)"


Energy minimization and the NVT equilibration ran without any error or
warning. The mdp file used is as shown below;

title                    = Martini
define                   = -DPOSRES
integrator               = md
dt                       = 0.02
nsteps                   = 50000
nstcomm                  = 10
comm-grps                =
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 100
nstxtcout                = 1000
xtc_precision            = 100
xtc-grps                 =
energygrps               = Protein W
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.4
coulombtype              = Shift
rcoulomb_switch          = 0.0
rcoulomb                 = 1.2
epsilon_r                = 15
vdw_type                 = Shift
rvdw_switch              = 0.9
rvdw                     = 1.2
tcoupl                   = v-rescale
tc-grps                  = System
tau_t                    = 1.0
ref_t                    = 300
Pcoupl                   = parrinello-rahman
Pcoupltype               = isotropic
tau_p                    = 5.0
compressibility          = 3e-4
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 473529
constraints              = none
constraint_algorithm     = Lincs
unconstrained_start      = no
lincs_order              = 4
lincs_warnangle          = 30

Also the water box after energy minimization showed some gaps towards the
edge of the box when visualized using VMD.


can anybody please help me on how to overcome this error?


Thank you,
with regards,
Anu