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 <[email protected]
<mailto:[email protected]>> 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
<[email protected] <mailto:[email protected]>> 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
F: +31-30-2537623
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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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