Re: [gmx-users] [pairs] vs [exclusions]

Hi Mark, thanks for the elaborate answer. If [pairs] are considered bonded interactions it's perfectly clear. Peter On 13/07/16 17:24, Mark Abraham wrote: > Hi, > > Maybe I missed the point earlier, but as e.g. 5.4.4 Exclusions section of > PDF reference manual says: > > "Extra exclusions

Re: [gmx-users] [pairs] vs [exclusions]

Hi, Maybe I missed the point earlier, but as e.g. 5.4.4 Exclusions section of PDF reference manual says: "Extra exclusions within a molecule can be added manually in a [ exclusions ] section. Each line should start with one atom index, followed by one or more atom indices. All *non-bonded*

Re: [gmx-users] [pairs] vs [exclusions]

Hi Xavier (and list), I think that's a good way of rephrasing my question ;) Anyway, I made a mock system with just 2 particles (included below). gmx dump'ing the two tprs (with and without exclusions) I can't tell the difference, apart from the number of exclusions generated: >>> diff

Re: [gmx-users] [pairs] vs [exclusions]

Hi Peter, Wouldn’t the exclusion act on the regular LJ and pairs add a different LJ(14)? With exclusions, do you have the regular LJ present? XAvier. > On 13 Jul 2016, at 13:17, Peter Kroon wrote: > > Hi Mark (and list), > > thanks for the ideas. > `gmx check -s1

Re: [gmx-users] [pairs] vs [exclusions]

Hi Mark (and list), thanks for the ideas. `gmx check -s1 with_excl.tpr -s2 no_excl.tpr` didn't tell me much, unfortunately: ... comparing blocka excls excls.nra (1944 - 1920) comparing groups ... I think this means that with_excl.tpr contains 22 more exclusions. Running gmx dump on both files

Re: [gmx-users] [pairs] vs [exclusions]

Hi, I don't know which acts first, but making a few such .tpr files and (hopefully) gmx check on them should make clear what happens. Or worst case gmx dump the .tpr and do a textual diff. You can probably make your life easier by playing around with atoms with high indices. Mark On Wed, Jul

[gmx-users] [pairs] vs [exclusions]

Dear list, I a have a short question on topologies, and the manual is somewhat unclear. If I have a topology which defines both an exclusion between an atom pair and a specific interaction between them using the [pairs] directive (function type 2), will they then have a non-bonded interaction, or