GROMACS Tutorial

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 typeB, chargeB, and massB headings had to correspond to a B-state of the molecule. As of GROMACS version 4.0, topology modifications for simple (de)couplings are no longer required (hooray!), but in the case of mutating one molecule to another, wherein bonded and nonbonded terms may change, the old-style modifications (the so-called "dual topology approach") would still be required. The GROMACS manual, section 5.8.4, provides an example of such a transformation.

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