[gmx-users] Error Found by Equilibration

[Lianxin Xin]

Hi, everyone,

We are simulating a pure DPPC bilayer with 128 lipids.

Now, we defined a box around the bilayer, and solvated, after solvating, we
removed water molecular between the bilayer.
Then, we did energy minimization for the system. However, when we got our
nvt.tpr file, and did NVT equilibration, there are errors found. Our input
file are adjusted by the Tutorial 2: KALP15 in DPPC.

Some Important Command we applied:

*Solvate:*


gmx grompp -f ions.mdp -c dppc128_solv_fix.gro -p topol_dppc.top -o ions.tpr


gmx genion -s ions.tpr -o dppc128_solv_ions.gro -p topol_dppc.top -pname NA
-nname CL -neutral



*Energy Minimization*


gmx grompp -f minim.mdp -c dppc128_solv_ions.gro -p topol_dppc.top -o em.tpr


gmx mdrun -v -deffnm em



*Equilibration (here found errors)*


gmx grompp -f nvt.mdp -c dppc128_solv_ions.gro -r dppc128_solv_ions.gro -p
topol_dppc.top -n index.ndx -o nvt.tpr


gmx mdrun -deffnm nvt


 *ERROR for Equilibration *:

step 198: Water molecule starting at atom 11939 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates



step 200: Water molecule starting at atom 11939 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.



step 200: Water molecule starting at atom 11939 can not be settled.

Check for bad contacts and/or reduce the timestep if appropriate.

Wrote pdb files with previous and current coordinates

Wrote pdb files with previous and current coordinates



step 201: Water molecule starting at atom 14015 can not be settled.



.

.

.



Fatal error:

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

This usually means that your system is not well equilibrated.


link are including these files.

1. dppc128_solv_fix.gro        Removed water molecular

2. dppc128_solv_ions.gro     Energy Minimization

3. topol_dppc.top                   Input topol file

4. nvt.mdp                              NVT  input file

https://drive.google.com/file/d/0B1E3Ulh4cGv7azhqejk1VmhHbW1QTS12bF9zTE5KQl9kb1Rv/view?usp=sharing
https://drive.google.com/file/d/0B1E3Ulh4cGv7MGZNQ1Zoc183X3N5djhYVncxSThRcmdhTkQ4/view?usp=sharing
https://drive.google.com/file/d/0B1E3Ulh4cGv7ejBkUkg2d1pIR0lGOVI4Yjg5ZXk4WG8wOTFN/view?usp=sharing
https://drive.google.com/file/d/0B1E3Ulh4cGv7YTB0d21HUnRZZHhjQ3AyYXplU1c3ejhGVU5R/view?usp=sharing