On 11/15/16 7:44 AM, Kamps, M. wrote:
Dear GMX-users,
I'm experiencing difficulty with my manually added atoms to create a
metallic surface within GROMACS. My goal is to create a surface (at this
point metallic, Al) and let it interact with a protein.
In my current situation I've only modelled the aluminium surface
(non-bonded surface). The EM drops to a minimum in only 8 steps (first red
flag?), the NVT and NPT equilibrium look ok, but during the MD run the
surface disassembles like it is made up of loose sand. There is no
interaction at all between my individual atoms. What did I do wrong? Or
what did I forget to do?
I created the surface by defining one single Aluminium atom in a pdb file,
which i converted via pdb2gmx. To enable this, I added a Al.rtp file to a
CHARMM27 forcefield, this file contains these lines:
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 1 1
[ AL ]
[ atoms ]
; name type charge chargegroup
AL AL 0.000 0
Furthermore, to the atomtypes.atp file I added this line:
AL 26.981539 ; Aluminium mass
To the ffnonbonded.itp file I added this line:
AL 13 26.981539 0.000 A 0.2617500000 0.300000
Where the last two numbers relate to the Lennard-Jones potential. Although
these values are not based on any scientific literature (at this point),
they should show some interaction?
Garbage in, garbage out. If you don't have a basis for knowing that these
parameters give reasonable behavior, "some interaction" may be exactly what
you're getting. Use real parameters, from literature, or otherwise derived
properly.
For instance, CHARMM-compatible metal parameters for FCC lattice structures can
be found in:
Hendrik Heinz, R. A. Vaia, B. L. Farmer and R. R. Naik, Accurate Simulation
of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12-6 and 9-6
Lennard-Jones Potentials, Journal of Physical Chemistry C, 2008, 112,
17281-17290.
When I put the atom into pdb2gmx this is my output Al.gro file:
ALUMINIUM
1
1AL AL 1 0.000 0.000 0.000
0.00000 0.00000 0.00000
This atom is then replicated with insert-molecules to form an FCC crystal,
using an xyz coordinate file. The result is a nicely stacked (small slab
of) surface consisting of 256 atoms. The topology file looks like this:
[ moleculetype ]
; Name nrexcl
AL 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 AL rtp AL q 0.0
1 AL 1 AL AL 1 0 26.9815 ;
qtot 0
Including the usual lines such as include water models, ion models etc..
The surface is then put in a box (with 1.5 nm distance to edges, in all
directions) and solvated with tip3p water molecules. Can someone help me?
If you have water, then you need to know if the assigned LJ parameters produce
meaningful interactions with water. Solve one problem at a time; deal with the
pure metal lattice and make sure its properties are reasonable. Then figure out
if those parameters are balanced with respect to water interactions.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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