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

[Justin Lemkul]

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

-- 
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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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