[gmx-users] Error Found by Equilibration

[Dallas Warren]

Did you look at the coordinate file using vmd or pymol and the
atoms/molecules noted by the error?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Tue, 22 Jan 2019 at 11:02, 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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