[gmx-users] water molecule cannot be settled
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 1 01:03:27 CEST 2009
Carla Jamous wrote:
> 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
> <mailto: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.
Hmm? Why would the atom numbers not be accurate? Perhaps they might be
out by one if there's a counting-from-zero vs counting-from-one
mismatch, but surely nothing worse than that... And how would gmxdump help?
Mark
> "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
> <mailto:Itamar.Kass at med.monash.edu.au>
> ============================================
>
>
> On Wed, Sep 30, 2009 at 1:14 AM, Manik Mayur <manik.mayur at gmail.com
> <mailto:manik.mayur at gmail.com>> wrote:
>
> 2009/9/29 Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>
> <mailto: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>
> <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
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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