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

[Steven Neumann]

I found something in ffnonbonded in OPLSAA ff

; These ion atomtypes are NOT part of OPLS, but since they are
; needed for some proteins or tutorial Argon simulations we have added them.
 Cu2+       Cu2+   29	63.54600     2.000       A    2.08470e-01  4.76976e+00
 Fe2+       Fe2+   26	55.84700     2.000       A    2.59400e-01  5.43920e-02
 Zn2+       Zn2+   30	65.37000     2.000       A    1.95200e-01  9.78219e-01
 Ar         Ar     18	39.94800     0.000       A    3.41000e-01  2.74580e-02

If they are not OPLS maybe it is possible to use them?

Steven

On Thu, Nov 15, 2012 at 4:34 PM, Steven Neumann <s.neumann08 at gmail.com> wrote:
> 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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