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

Jon Kapla jon.kapla at mmk.su.se
Mon May 12 13:46:31 CEST 2014


There have been some efforts of trying to implement the 56Acarbo before, 
and there are some files that you might want to take a look at in the 
user contributions section on the Gromacs website. I think the files 
there only delas with 1-4 glycosidic linkages, but I guess it should be 
straightforward to extend it to other connections using the dihedral 
types from the 56Acarbo paper. Anyway the files might come in handy for 
you if you haven't dicovered them yet. I can't say anything about the 
quality of the conversion though, since I haven't used those parameters 
myself, but it seems they use the same approach as you do (and as I did 
a couple of years ago trying to accomplish the same thing, but I swiched 
to Glycam parameters before I finished the project). I guess the best 
thing would be to try to get hold of single point energies from gromos 
and compare them with your conversion.


Jon Kapla

On 2014-05-12 12:49, Hardy, Adam wrote:
> 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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