[gmx-users] Cannot minimiza - vdwradii.dat ???
s.neumann08 at gmail.com
Thu Nov 15 17:34:32 CET 2012
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:
>>>> FE 55.84700 ; heme iron 56
>>>> FE 9 18.998 0.000 A 0.115816833358244 -0
>>>> [ FE ]
>>>> [ atoms ]
>>>> FE FE 2.00 0
>>>> Hmmmm, confusing...
>>> What force field is that? None of those parameters seem to come from any
>>> the default force fields in Gromacs. The entry in ffnonbonded is clearly
>>> wrong, with the parameters appearing to belong to fluorine rather than
>>> but the line appears to have been mangled. It looks most like CHARMM,
>>> someone has messed with ffnonbonded.itp.
>>> Regardless, if you look at the parameters for FE in any of the force
>>> 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
>>> free ions makes little sense.
>> This is charmm27 but modified as you can see. Shall I use:
>> FE 26 55.84700 2.000 A 0.115816833358 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
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?
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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