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

[Peter Kroon]

Hi Sudip,


there's a dedicated forum for these Martini questions on cgmartini.nl.
Recently there was a similar question there
(http://cgmartini.nl/index.php/component/kunena/7-mdp-options/5491-gpu-verlet-oscillational-period#7308).

To summarize, the bonds between the backbone beads are extremely stiff.
If your protein is small/short enough you can change them to
constraints. I'll start a discussion in the group here on how to handle
it further.


Peter


On 29-06-17 09:06, Sudip Das wrote:
> 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