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

[Steven Neumann]

On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/15/12 10:55 AM, Steven Neumann wrote:
>>
>> On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>
>>> On 11/15/12 10:41 AM, Steven Neumann wrote:
>>>>
>>>>
>>>> atomtypes.atp
>>>>
>>>> FE      55.84700 ;      heme iron 56
>>>>
>>>> ffnonbonded
>>>>
>>>> FE     9      18.998    0.000   A     0.115816833358244  -0
>>>>
>>>> aminoacids.rtp
>>>>
>>>> [ FE ]
>>>>    [ atoms ]
>>>>          FE      FE      2.00    0
>>>>
>>>>
>>>> Hmmmm, confusing...
>>>>
>>>
>>> What force field is that?  None of those parameters seem to come from any
>>> of
>>> the default force fields in Gromacs. The entry in ffnonbonded is clearly
>>> wrong, with the parameters appearing to belong to fluorine rather than
>>> iron,
>>> but the line appears to have been mangled.  It looks most like CHARMM,
>>> but
>>> someone has messed with ffnonbonded.itp.
>>>
>>> Regardless, if you look at the parameters for FE in any of the force
>>> fields
>>> in Gromacs, you will see that their nonbonded parameters (C6/C12 or
>>> sigma/epsilon) are generally set to zero.  They interact only via ionic
>>> interactions because they were likely only intended for use in cofactors
>>> like heme, where other bonded parameters fix their geometry.  Using them
>>> as
>>> free ions makes little sense.
>>>
>>>
>>> -Justin
>>>
>>
>> This is charmm27 but modified as you can see. Shall I use:
>>
>> FE      26      55.84700        2.000   A       0.115816833358  0
>> 0
>>
>> in original Gromacs charmm it is
>>
>> FE      26      55.84700        0.000   A       0.115816833358  0.0 ;
>> partial charge def not found
>>
>
> These changes will have no effect and will not solve your problem.  The
> charge field in ffnonbonded.itp is never used for anything.  I don't know
> what the extra zero is intended for, but it will probably break the ability
> of grompp to read the file.
>
> Moreover, the point of my previous comments was that your use of this atom
> type is not appropriate.  The FE atom type still has zero repulsive
> interactions, unless explicitly calculated with each atom type.  As far as I
> can tell from ffnonbonded.itp, this repulsive term is zero for every
> interaction, meaning no matter what you do, your Fe ions will always collide
> with something negatively charged because there are no LJ terms to impede
> the Coulombic attraction, leading to an infinitely negative potential at a
> fixed point and thus the crash.
>
> You need to find better parameters entirely if you wish to simulate free Fe
> ions.
>
> -Justin

Thank you for this. I will try to look at Charmm forum for those
parameters. I was also thinking about parameters which Zn(2+) has got
as they have similar mass. What do you think?

Steven

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