[gmx-users] No interaction between manually added atoms
jalemkul at vt.edu
Wed Nov 16 03:25:45 CET 2016
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
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:
> 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 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
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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