[gmx-users] CGMD simulation is not running with antifreeze water beads and 20 fs timestep

[Sudip Das]

Dear All,

I am running a CGMD simulation of protein and surfactant in water with
Martini2.0 force field for surfactant and water and ELNEDYN2.2 force field
for protein.

The system is running fine with 20 fs integration timestep. But it leads to
solid phase of water. So, I have introduce antifreeze water beads (which
are 10% in number w.r.t. the total number of water beads). But after this,
simulation is not at all running with 20 fs timestep and gives the error:

segmentation fault (signal 11)

Within output file, it shows:

Step 2, time 0.04 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.007237, max 0.028381 (between atoms 20 and 21)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
     20     21   30.4    0.1981   0.1895      0.1950


I have tried to solve it in several ways, i.e., decreasing the time steps
(it is running fine with 2 fs), equilibrating the system properly,
compiling and running in serial version of gromacs (to test whether the
error comes due to domain decomposition during parallel run) etc. Even
though, I am getting the same error.

While compiling the job with grompp, I got the below warning:

WARNING 1 [file system.top, line 18]:
  The bond in molecule-type Protein_A between atoms 1 BB and 2 BB has an
  estimated oscillational period of 9.7e-02 ps, which is less than 5 times
  the time step of 2.0e-02 ps.
  Maybe you forgot to change the constraints mdp option.

But, following the link
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-May/089120.html
, I have ignored this warning using -maxwarn flag. Probably this wouldn't
be the cause for this error, as I got exactly the same warning for the
system without antifreeze water beads.


Please help me to solve this problem. I would be happy to share my files if
needed.

Thanks in advance!

Best regards.
Sudip