Step Two: Examine the Topology
Download the coordinate file and topology for this system. These files were provided as part of David Mobley's tutorial for this system (which is no longer online), and are the original files (modified slightly for compatibility with recent GROMACS versions) used by Michael Shirts in the paper referenced on the previous page.
The system contains a single molecule of methane (called "ALAB" in the coordinate file, for the β-carbon of alanine) in a box of 596 TIP3P water molecules. Looking into the topology, we find:
; Topology for methane in TIP3P #include "oplsaa.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Methane 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_138 1 ALAB CB 1 0.000 12.011 2 opls_140 1 ALAB HB1 2 0.000 1.008 3 opls_140 1 ALAB HB2 3 0.000 1.008 4 opls_140 1 ALAB HB3 4 0.000 1.008 5 opls_140 1 ALAB HB4 5 0.000 1.008 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 1 5 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 2 1 4 1 2 1 5 1 3 1 4 1 3 1 5 1 4 1 5 1 ; water topology #include "oplsaa.ff/tip3p.itp" [ system ] ; Name Methane in water [ molecules ] ; Compound #mols Methane 1 SOL 596
You will note that all charges are set to zero. There is a practial reason behind this setup. Normally, charge interactions between the solute and water are turned off prior to the van der Waals terms. If charge interactions are left on when Lennard-Jones terms are turned off, positive and negative charges would be allowed to approach one another at infinitely close distances, resulting in a very unstable system that would probably just blow up. The procedure in this tutorial essentially assumes that charges have been properly been turned off prior to this point, and we will be turning off only van der Waals interactions between the solute and solvent.
Note that in previous versions of GROMACS, the contents of the
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