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

[Sudip Das]

Hi Peter,

Sorry for the delay. According to your suggestion, I have equilibrated my
system with gradually increasing time step (1, 2, 5, 10, 15, 20 fs). After
that, the production step is running successfully.

Thanks a lot for your kind help!

Best regards,
Sudip

On Thu, Jun 29, 2017 at 2:32 PM, Peter Kroon <p.c.kroon at rug.nl> wrote:

> Hi Sudip,
>
>
> we had a short discussion over coffee. We also get these warnings, but
> they don't generally lead to significant instabilities. This means you
> probably have an equilibration issue. Could you try equilibrating your
> system with increasing timesteps? So first equilibrate with 5fs, then
> continue with 10 fs, 15fs and finally 20 fs.
>
> If that doesn't work, could you give a more detailed description of your
> system?
>
>
> Peter
>
>
> On 29-06-17 10:07, Peter Kroon wrote:
> > 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
> >
>
>
>
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