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

[Justin Lemkul]

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

-- 
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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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