[gmx-users] Cannot minimiza - vdwradii.dat ???

[Steven Neumann]

Please, see final coordinates.

  94LIG     O1  787   0.482   5.056   3.507
  94LIG     FE  805   0.432   5.011   3.039

How is that possible?

On Thu, Nov 15, 2012 at 3:26 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> I tried both options and now different atom is responsible of this
> (Oxygen from small molecule next to Fe). With nstxout = 1 I observed
> the trajectory -> My Fe(2+) is coming very close to the Oxygen atom
> and it looks that their coordinate became equal: in VMD Oxygen absorbs
> Fe(2+) and the atom disappears :) Any suggestions?
>
> Steven
>
> On Thu, Nov 15, 2012 at 3:03 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
>> :))))))))))))
>>
>> On Thu, Nov 15, 2012 at 2:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>> On 11/15/12 9:57 AM, Steven Neumann wrote:
>>>>
>>>> On Thu, Nov 15, 2012 at 2:35 PM, Steven Neumann <s.neumann08 at gmail.com>
>>>> wrote:
>>>>>
>>>>> I will. Thank you.
>>>>>
>>>>> Steven
>>>>>
>>>>> On Thu, Nov 15, 2012 at 2:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 11/15/12 9:03 AM, Steven Neumann wrote:
>>>>>>>
>>>>>>>
>>>>>>> On Thu, Nov 15, 2012 at 1:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On 11/15/12 8:41 AM, Steven Neumann wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Dear Gmx Users,
>>>>>>>>>
>>>>>>>>> I am trying to run simulations of protein and FE(2+) atoms. I placed
>>>>>>>>> them randomly around the protein, solvated the system and tried to
>>>>>>>>> minimize. After grompp, I tried mdrun:
>>>>>>>>>
>>>>>>>>> Stepsize too small, or no change in energy.
>>>>>>>>> Converged to machine precision,
>>>>>>>>> but not to the requested precision Fmax < 1000
>>>>>>>>>
>>>>>>>>> Double precision normally gives you higher accuracy.
>>>>>>>>> You might need to increase your constraint accuracy, or turn
>>>>>>>>> off constraints alltogether (set constraints = none in mdp file)
>>>>>>>>>
>>>>>>>>> Steepest Descents converged to machine precision in 62 steps,
>>>>>>>>> but did not reach the requested Fmax < 1000.
>>>>>>>>> Potential Energy  = -7.2573600e+05
>>>>>>>>> Maximum force     =  5.7863950e+05 on atom 756
>>>>>>>>> Norm of force     =  3.5862925e+03
>>>>>>>>>
>>>>>>>>> I tried different stepsizes, constarint = none etc but never
>>>>>>>>> converged
>>>>>>>>> to requested Fmax < 1000
>>>>>>>>>
>>>>>>>>> When I try NVT:
>>>>>>>>>
>>>>>>>>> Fatal error:
>>>>>>>>> 2 particles communicated to PME node 0 are more than 2/3 times the
>>>>>>>>> cut-off out of the domain decomposition cell of their charge group in
>>>>>>>>> dimension x.
>>>>>>>>> This usually means that your system is not well equilibrated.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> So the problem is with minimization.
>>>>>>>>>
>>>>>>>>> My question: Can it be the problem of not specified vdwradius of my
>>>>>>>>> FE(2+) in vdwradii.dat ? I mean, can ater molecules overlap with
>>>>>>>>> Ferrous and thus minimization does not converge?
>>>>>>>>>
>>>>>>>>
>>>>>>>> The problem is unrelated to vdwradii.dat, which is only used for
>>>>>>>> neighbor
>>>>>>>> searching with genbox.  mdrun tells you there is a problem with atom
>>>>>>>> 756.
>>>>>>>> What is it?  What is it interacting with?  That's how you trace the
>>>>>>>> problem.
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>
>>>>>>> This is Fe(2+) - from trjactory it can be observed that it collides
>>>>>>> with negatively charged oxygen from my other small molecule. Are you
>>>>>>> sure that vdwradii.dat wont solve it while placing molecules using
>>>>>>> genbox and then solvating. The vdw radius of Fe(2+) is 2 A. Would you
>>>>>>> suggest something?
>>>>>>>
>>>>>>
>>>>>> Try it and see.  If genbox doesn't find a radius, it uses a default
>>>>>> value,
>>>>>> which is specified with -vdwd on the command line, so modifications to
>>>>>> vdwradii.dat are not strictly necessary, but a more explicit command
>>>>>> might
>>>>>> be.
>>>>>>
>>>>>> -Justin
>>>>
>>>>
>>>> If change -vdwd to 0.2 it will affect slo water molecules which is not
>>>> desirable. Shall I just copy vdwradii.dat to my working directory and
>>>> add:
>>>>
>>>>
>>>> ???  FE    0.20
>>>>
>>>> Will that change it?
>>>>
>>>
>>> Yes.
>>>
>>> -Justin
>>>
>>>
>>> --
>>> ========================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> 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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