[gmx-users] water molecule cannot be settled
Itamar Kass
itamar.kass at gmail.com
Thu Oct 1 03:33:04 CEST 2009
Hi,
I found that in big system, when I work with pdb files I have to use
gmxdump in order to find out which atom the number mean.
Itamar
On 01/10/2009, at 9:03 AM, Mark Abraham wrote:
> 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
>> 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 <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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