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? 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? Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.