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

[Peter Kroon]

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
>