[gmx-users] Error Found by Equilibration

[Mark Abraham]

Hi,

Minimization is sometimes not enough to stop
http://manual.gromacs.org/current/user-guide/terminology.html#blowing-up.
Start with a smaller timestep while you let the large forces relax. Then
move to your production setup.

Mark

On Tue, 22 Jan 2019 at 01:02 Lianxin Xin <lxin9519 at gmail.com> wrote:

> 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
> --
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