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

[Steven Neumann]

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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