[gmx-users] (no subject)

[Christian Blau]

Hello Saranya,

Now again with readable formatting. Also note that it is very useful to people on gmx-useres to  specify the subject when writing emails, because it makes it easier to search, reply, and handle multiple discussion threads.

This error means that during the nvt equilibrium high forces occurred that made it impossible to resolve the bond constraints. The very high forces occurred most likely are due to some high tension in the system.

As indicated in the error message you can:
  - Reduce the time step of your run initially to relax the structure first.
  - Check the output PDB structure at the site where the error occurred (atoms 217 and 218), possibly removing or displacing the offending water molecule manually
  - Check that you used a well relaxed structure from energy minimisation

Best,
Christian

On 11/1/19 7:48 AM, saranya wrote:
> Hello everyone,
> while running nvt equilibration i am getting the error as:
> Step 12, time 0.024 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms nan, max 92522.640625 (between atoms 217 and 218)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>      277    278   58.9    0.1090  74.2482      0.1090
>      281    282   35.8    0.1098  73.5336      0.1090
>      281    283  119.3    0.1097  74.0780      0.1090
>      281    284   63.5    0.1097  74.2253      0.1090
>
> step 12: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> Back Off! I just backed up step12b.pdb to ./#step12b.pdb.1#
>
> Back Off! I just backed up step12c.pdb to ./#step12c.pdb.1#
> Wrote pdb files with previous and current coordinates
> Segmentation fault (core dumped)
>
>
>
> how can i resolve this error...?
>
> With Regards,
>
> *Saranya Vasudevan,*
>
> *Research Scholar,*
>
> *Molecular Quantum Mechanics Laboratory,*
>
> *Department of Physics,*
>
> *Bharathiar University,*
>
> *Coimbatore-46*