On 11/15/12 10:55 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 3:47 PM, Justin Lemkul <[email protected]> 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
--
========================================
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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