[gmx-users] water molecule can not be settled,what could be the cause?

[T.A.Wassenaar]

Hi Jian Zou,

One reason for this may be that a water molecule is 
trapped inside a protein. It can start to oscillate and at 
a certain moment jump to overlap with the protein, causing 
the failure. If you find a single water molecule buried 
inside your protein after using genbox, you may want to 
remove it (or several single water molecules). It is also 
possible that you're suffering from problems related to 
the box, for that it's necessary to know the box type you 
use, the version of gromacs and the .mdbp file you use. 
But first try the other thing :)

Hope it helps,

Tsjerk

On Fri, 3 Jun 2005 09:54:25 +0800
  "Jian Zou" <zouj01 at mails.tsinghua.edu.cn> wrote:
> Hi all,
> 
> My simulation halts, and the log file reads
> 
> t = 238.148 ps: Water molecule starting at atom 6051 can 
>not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote 
>pdb files with previous
> and current coordinates
> 
> t = 238.150 ps: Water molecule starting at atom 7218 can 
>not be settled.
> Check for bad contacts and/or reduce the timestep.Wrote 
>pdb files with previous
> and current coordinates
> 
> 
> I use dt=1fs, T=400K, P=3bar for this simulation.
> The initial structure is taken as the final structure of 
>20ps PR-MD.
> 
> I also rerun this simulation, but the same thing happend 
>at almost the same time (t=230-240ps).
> 
> 
> What could be the cause for the above failure in my 
>simulation?
> Box size too small?
> Could anybody give me some hint to work this problem 
>out?
> 
> 
> Thank you very much for your comment.
> 
> 
> Regards,
> 
> Jian Zou
> 
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