[gmx-users] water molecule cannot be settled
Mark Abraham
Mark.Abraham at anu.edu.au
Thu Oct 1 03:42:26 CEST 2009
Itamar Kass wrote:
> 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.
But it's the same atom name as in the coordinate file you supplied to
grompp, and as is written at the end of mdrun. gmxdump on your .tpr
might only be needed if you didn't have these!
Mark
> 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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