[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes

Thu Jun 19 07:44:58 CEST 2014

ok, I tried with an arbitrary value of kb for all the harmonic bonds
(7150000) and the distances as they are in the crystal structure.  There
are 5 harmonic bonds with FE which I defined in the itp, but I am getting
an error on one of them while doing position restrained MD for 50 ps. I
tried with both the constraints = none / hbond , but getting the same
error. (Here, I have turned on the temperature coupling as well)

*The bond in molecule-type Protein_chain_A between atoms 4207 FE and 2546
NE2 has an estimated oscillational period of 7.9e-03 ps, which is less
than 5 times the time step of 2.0e-03 ps.  Maybe you forgot to change the
constraints mdp option.*

Can you please suggest where might be the problem?

Thanks,
Sucharita

On Wed, Jun 18, 2014 at 7:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/18/14, 6:47 AM, sucharita dey wrote:
>
>> Thanks Justin. The OGA topology is now OK. But still the problem with the
>> FE ion persists (very high force on it) during the minimization.
>> Yes, I want to link the FE with its co-ordination atoms by simple harmonic
>> (bond type 6), can you please tell what will be the value for kb (the
>> force
>> constant)?
>>
>>
> No idea.  If there are no vibrational data available for the interaction,
> you're stuck with using some arbitrary value.  That's actually somewhat
> common when dealing with transition metals, because that's the least of
> your worries when it comes to such species; MM representations of such
> metals are very poor in general.
>
> -Justin
>
>
>
>> On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 6/13/14, 2:11 AM, sucharita dey wrote:
>>>
>>>  Dear Users,
>>>>
>>>> I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG
>>>> (N-OxalyGlycine) and crystal waters.
>>>>
>>>> I have generated the initial topology of OGA from PRODRG and
>>>> incorporated
>>>> it in the  the forcefield gromos 53a6 and since the forcefield already
>>>> has
>>>> parametrs for ZN and FE, I had no problem in generating the  *.itp
>>>> files.
>>>> I
>>>> solvated the system and ran steep minimization for 1000 steps with
>>>> emstep
>>>> =
>>>> 0.1 and emtol 1.
>>>>
>>>>
>>>>  Is the NOG topology sound?  PRODRG has known problems getting charges
>>> right, but building a suitable NOG topology from existing building blocks
>>> is trivial.
>>>
>>>
>>>   It ran for ~80 steps and stopped. I checked the gro file generated, the
>>>
>>>> problem is around OGA and the FE,  and the OGA is loosing its
>>>> structure. I
>>>> suspect it due to clashes, -- actually in the crystal structure 2
>>>> oxygens
>>>> of OGA are in co-ordination with the FE (the FE being co-ordinated with
>>>> 4
>>>> other atoms including one O from crystal water).
>>>>
>>>>
>>>>  Sounds like a potential topology issue.  One simple test is to run NOG
>>> in
>>> vacuo then in a box of water to see if it is stable on its own, then deal
>>> with it in the context of the full protein+ions.
>>>
>>>
>>>   I have not considered the FE co-ordination, can you please suggest how
>>> to
>>>
>>>> do this or else please suggest if you feel the problem is elsewhere.
>>>>
>>>>
>>>>  Ion coordination is easily done with distance restraints or type-6
>>> harmonic connections.
>>>
>>>   Below is the comment given after minimization stopped:
>>>
>>>>
>>>> *Energy minimization has stopped, but the forces havenot converged to
>>>> therequested precision Fmax < 1 (whichmay not be possible for your
>>>> system).
>>>> Itstoppedbecause the algorithm tried to make a new step whose sizewas
>>>> toosmall, or there was no change in the energy sincelast step. Either
>>>> way,
>>>> weregard the minimization asconverged to within the available
>>>> machineprecision,given your starting configuration and EM
>>>> parameters.Double
>>>>
>>>> precision normally gives you higher accuracy, butthis is often notneeded
>>>> for preparing to run moleculardynamics.writing lowest energy
>>>> coordinates.Steepest Descents converged to machine precision in 84
>>>> steps,but did not reach the requested Fmax < 1.Potential Energy  =
>>>> -3.7139549e+08Maximum force     =  7.7602650e+14 on atom 4207Norm of
>>>> force     =  3.6179670e+12*
>>>>
>>>> NOTE: the atom 4207 with maximum force is FE
>>>>
>>>>
>>>>  You have essentially infinite forces, which indicate very bad geometry,
>>> clashes, or a bad topology.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 601
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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> Gromacs Users mailing list
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