[gmx-users] equilibration_error

[Antonio Carlesso]

Hi all,

Is there any general tips to follow when system (protein + ligand
complexes) is not well equilibrated?



The energy minimization was performed. The system crash during NVT
equilibration..



 Major error below..



*aprun -n 32 gmx_mpi mdrun -deffnm nvt*



*Step 0, time 0 (ps)  LINCS WARNING*

*relative constraint deviation after LINCS:*

*rms 0.001553, max 0.026948 (between atoms 21788 and 21789)*

*bonds that rotated more than 30 degrees:*

* atom 1 atom 2  angle  previous, current, constraint length*

starting mdrun 'model_crystal_plus_kira'

100000 steps,    200.0 ps.



*Step 0, time 0 (ps)  LINCS WARNING*

*relative constraint deviation after LINCS:*

*rms 0.522030, max 12.841240 (between atoms 21786 and 21787)*

*bonds that rotated more than 30 degrees:*

* atom 1 atom 2  angle  previous, current, constraint length*

*Step 1, time 0.002 (ps)  LINCS WARNING*

*relative constraint deviation after LINCS:*

*rms 51.315476, max 1190.019043 (between atoms 21319 and 21320)*

*bonds that rotated more than 30 degrees:*

* atom 1 atom 2  angle  previous, current, constraint length*



*Step 1, time 0.002 (ps)  LINCS WARNING*

*relative constraint deviation after LINCS:*

*rms 0.033181, max 0.912026 (between atoms 20924 and 20925)*

*  21367  21369   43.8    0.1526   0.1545      0.1526*

*bonds that rotated more than 30 degrees:*

* atom 1 atom 2  angle  previous, current, constraint length*



*Step 1, time 0.002 (ps)  LINCS WARNING*

*relative constraint deviation after LINCS:*

*rms 16578759.232898, max 966054976.000000 (between atoms 21788 and 21789)*

*bonds that rotated more than 30 degrees:*

* atom 1 atom 2  angle  previous, current, constraint length*



Back Off! I just backed up step1b_n26.pdb to ./#step1b_n26.pdb.1#



Back Off! I just backed up step1b_n29.pdb to ./#step1b_n29.pdb.2#



Back Off! I just backed up step1b_n25.pdb to ./#step1b_n25.pdb.2#



Back Off! I just backed up step1c_n26.pdb to ./#step1c_n26.pdb.1#



Back Off! I just backed up step1c_n29.pdb to ./#step1c_n29.pdb.2#

-------------------------------------------------------



*Fatal error:*

*12 particles communicated to PME rank 6 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.*

*This usually means that your system is not well equilibrated.*

*For more information and tips for troubleshooting, please check the
GROMACS*

*website at **http://www.gromacs.org/Documentation/Errors
<http://www.gromacs.org/Documentation/Errors>*

*-------------------------------------------------------*



*WARNING: Listed nonbonded interaction between particles 21318 and 21320*

*at distance 4.410 which is larger than the table limit 2.036 nm.*



*This is likely either a 1,4 interaction, or a listed interaction inside*

*a smaller molecule you are decoupling during a free energy calculation.*

*Since interactions at distances beyond the table cannot be computed,*

*they are skipped until they are inside the table limit again. You will*

*only see this message once, even if it occurs for several interactions.*



*IMPORTANT: This should not happen in a stable simulation, so there is*

*probably something wrong with your system. Only change the table-extension*

*distance in the mdp file if you are really sure that is the reason.*



*WARNING: Listed nonbonded interaction between particles 20873 and 20885*

*at distance 1317.737 which is larger than the table limit 2.036 nm.*



*This is likely either a 1,4 interaction, or a listed interaction inside*

*a smaller molecule you are decoupling during a free energy calculation.*

*Since interactions at distances beyond the table cannot be computed,*

*they are skipped until they are inside the table limit again. You will*

*only see this message once, even if it occurs for several interactions.*



*IMPORTANT: This should not happen in a stable simulation, so there is*

*probably something wrong with your system. Only change the table-extension*

*distance in the mdp file if you are really sure that is the reason.*