[gmx-users] Exclusion and 1-4 interactions with tabulated potential

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 5 14:15:28 CEST 2009

Johannes Kamp wrote:
> Hi @ all,
> I'm a little confused about 1-4 interactions at the moment and I hope 
> you can help me along...
> I'm using tabulated potentials for bonded and non-bonded potentials with 
> the Martini FF. The 1-4 interactions are fully represented by the 
> non-bonded potential,

Rather than "fully", if they're "only" represented with the non-bonded 
potential, then you merely have to address whether they're scaled or 
not. The "generate pairs" mechanism is useful in the former case - it 
generates a list of atom pairs for which the nonbonded interactions are 
generated from the usual potential scaled by the fudge factors, except 
that [pairs] specified in the .top are not over-ridden. Presumably 
nrexcl = 3 directs pair generation for 1-4 interactions... I'd guess 
nrexcl = 2 might direct pair generation for 1-3...

> charged particles are not present. I implemented 
> the non-bonded potential with -table option in mdrun. After reading 
> chapter 4.6.1 and 5.7.1 of the manual about exclusion and 1-4 
> interactions the following confused me:
> I set the neighbor exclusion nrexcl = 3. Is that correct if I've got the 
> 1-4 interactions represented in my non-bonded potential, or do I have to 
> set nrexcl = 2?

nrexcl = 3 means no 1-4 interactions are generated (see for example 
footnote to table 5.3 in 5.7.1). If you wanted them, either in normal or 
scaled form, you'd have to supply them in a separate pair list, or use 
nrexcl = 2. The third para of 4.6.1 says this.

> Furthermore in chapter 4.6.1 something is said about a reducing factor 
> of two, do I have to use it? -I'm asking because in my simulations 
> everything clots together, thus the nb Forces seem to be too strong.

Read the forcefield paper/documentation/whatever to find the answer this.


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