[gmx-users] water molecule cannot be settled

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 14:05:25 CEST 2009



Carla Jamous wrote:
> 
> Thank you for your reply,
> but none of the water molecules with error messages is trapped inside my 
> protein, nor is it in contact with the protein or the ions in my system.
> 

Then you need to watch the trajectory and see where things go wrong.  In 
unstable systems, I often set "nstxout = 1" to capture as many frames in the 
.trr file as possible (if the crash is happening early, as it is in your case).

Likely, energy minimization did not resolve all the bad contacts, but may still 
have converged within your criteria.  You could also specify a lower target Fmax 
during EM to see if things resolve.

-Justin

> Carla
> 
> On Tue, Sep 29, 2009 at 1:15 PM, Tsjerk Wassenaar <tsjerkw at gmail.com 
> <mailto:tsjerkw at gmail.com>> wrote:
> 
>     Hi Carla,
> 
>     You may have a water molecule trapped inside your protein. Check the
>     water molecule with the given atom number in a viewer, together with
>     your structure. If it is inside, you can try to remove it manually
>     from the system, editing the structure file and decreasing the amount
>     of solvent listed in te topology file. If you edit the .gro file, do
>     mind to decrease the number on the second line (the number of atoms)
>     by three.
> 
>     Hope it helps,
> 
>     Tsjerk
> 
>     On Tue, Sep 29, 2009 at 11:38 AM, Carla Jamous
>     <carlajamous at gmail.com <mailto:carlajamous at gmail.com>> wrote:
>      > Hi,
>      > I have a problem with water molecules in my system: I'm using
>     Gromacs with
>      > ffamber94 force-field. During minimization, I have this message:
>      >
>      > t = 0.014 ps: Water molecule starting at atom 10045 can not be
>     settled.
>      > Check for bad contacts and/or reduce the timestep.Wrote pdb files
>     with
>      > previous and current coordinates
>      >
>      > The minimization converged. However, molecular dynamics were stopped.
>      > I tried minimization with different parameters: Flexible,
>      > position-restrained, reducing my timestep, etc... and nothing worked.
>      >
>      > I also tried one simulation with TIP3P water model and another
>     simulation
>      > with SPC water model and I still get the same error.
>      > I tried to access: oldwiki.gromacs.org
>     <http://oldwiki.gromacs.org> but access is denied.
>      >
>      > Please does anyone have a solution to propose?
>      >
>      > Thanks
>      > Carla
>      >
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> 
> 
> 
>     --
>     Tsjerk A. Wassenaar, Ph.D.
>     Junior UD (post-doc)
>     Biomolecular NMR, Bijvoet Center
>     Utrecht University
>     Padualaan 8
>     3584 CH Utrecht
>     The Netherlands
>     P: +31-30-2539931
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> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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