[gmx-users] gen-pairs, nrexcl and [ pairs ] in itp files

Hardy, Adam ah259 at hw.ac.uk
Mon May 12 12:50:35 CEST 2014

Dear All,

I am attempting to make modifications to the Gromos 53A6 forcefield in order to implement the Gromos 56Acarbo forcefield in GROMACS. Most of the modifications are straightforward except for some of the LJ parameters. As well as simple adjustments to most of the 1-4 interaction parameters there is a requirement to implement a) some 1-4 interaction parameters when the 2 and 3 atoms are specific combinations and b) some 1-5 special parameters.

As I'm fairly new to GROMACS I was hoping someone could verify my method and clarify one or two things.

I would need to set nrexcl to 4 in order to stop the special 1-5 parameters being calculated twice (once "normal" LJ, one "special").

In the itp file I would then need to explicitly provide all the special 1-4 and all the 1-5 LJ parameters (in addition to listing the normal 1-4 interaction pairs) as GROMACS cannot look these up in the forcefield files.

If gen-pairs is set to yes, does it overwrite parameters given in the itp file? This way I would not have to go through and explicitly list the "normal" 1-4 interaction parameters in the itp file.

I hope that is clear.

Many thanks in advance,

Adam Hardy
PhD Student
School of Engineering and Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS, UK

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