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

[Steven Neumann]

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