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

[Justin Lemkul]

On 11/15/12 10:29 AM, Steven Neumann wrote:
> 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?
>

Please see my previous post and answer the question regarding the source of your 
Fe parameters.

-Justin

> 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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-- 
========================================

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

========================================