[gmx-users] water molecule cannot be settled
Carla Jamous
carlajamous at gmail.com
Wed Sep 30 14:29:45 CEST 2009
Hi,
what do you mean: "use gmxdump to trace the molecule"?
I'm a beginner with gromacs and all I found about gmxdump is that it reads a
binary file & prints that to standard output in a readable format.
So how can I check if my atom number is the same in my pdb file & my output
file?
Carla
On Wed, Sep 30, 2009 at 4:38 AM, Itamar Kass <itamar.kass at gmail.com> wrote:
> Hi,
>
> another point you should consider is that the atom/molecule number in the
> pdb or gro file are not necessarally the what you see in your output. You
> should use gmxdump in such cases to trace the molecule.
>
>
> Cheers,
> Itamar
>
> ---
>
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at med.monash.edu.au
> ============================================
>
>
> On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <manik.mayur at gmail.com>wrote:
>
>> 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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>>
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