[gmx-users] water molecule cannot be settled

[Manik Mayur]

2009/9/29 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> 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.
>>
>>
Also if the water molecules are positioned properly, you can try define =
-DPOSRES_WATER in your .mdp file with a high value set in your
topology(.top) file under [position restraint] section as,

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       100000       100000       100000
#endif

-Manik

 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
>>    F: +31-30-2537623
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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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