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

[Steven Neumann]

:))))))))))))

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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