[gmx-users] Segmentation fault during equilibration

[Yasser Almeida]

Hi all,

I am running an equilibration of a membrane/protein coarse grained 
system and got this Segmentation fault error.

---
Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single 
precision)
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this 
machine, which is better)
starting mdrun 'Protein in INSANE! Membrane UpperLeaflet>DPPC=1 
LowerLeaflet>DPPC=1'
25000 steps,    500.0 ps.
step 0
Step 3, time 0.06 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000001, max 0.000003 (between atoms 204 and 205)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      30     31   32.7    0.1950   0.1950      0.1950

Step 4, time 0.08 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 195678.573993, max 1044637.687500 (between atoms 30 and 31)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
      30     31   90.0    0.1950 203704.5469      0.1950
Wrote pdb files with previous and current coordinates
Segmentation fault (core dumped)
---

This is the mdp file:
---
dt         =  0.02
nsteps       =  25000
nstxout      =  0
nstvout      =  0
nstlog       =  100
nstxtcout     =  100
xtc-precision     =  100
rlist         =  1.4
coulombtype     =  shift
rcoulomb     =  1.2
epsilon_r     =  15
vdw-type     =  shift
rvdw-switch     =  0.9
rvdw         =  1.2
tcoupl       =  v-rescale
tc-grps      =  Protein_DPPC W_Ion
tau-t         =  1.0 1.0
ref-t         =  323 323
Pcoupl       =  berendsen
Pcoupltype     =  semiisotropic
tau-p         =  10.0 10.0
compressibility  =  3e-4 3e-4
ref-p         =  1.0 1.0
refcoord_scaling =  com
---

I've used this settings before with similar protein/membrane systems 
without problem.

Any thoughts?
Thanks in advance

Yasser

-- 
Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
Germany
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c