On 11/15/12 11:34 AM, Steven Neumann wrote:
On Thu, Nov 15, 2012 at 4:03 PM, Justin Lemkul <[email protected]> wrote:
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
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?
For almost every element in the periodic table, you can find another element
with a similar mass. That doesn't mean their nonbonded parameters will be of
any use. A 20% difference between iron and zinc is non-negligible, anyway ;)
More importantly, transition elements are very challenging, and their behavior
is governed by a lot more than just the naive MM representation of a sphere of
fixed charge.
-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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