[gmx-developers] F_BONDS vs F_CONSTR

Berk Hess hess at kth.se
Wed Nov 25 14:35:46 CET 2015

I don't understand what you mean with "same data". In your particular 
case maybe yes.
The user can manually enter bonds and/or constaints in the topology.
In the common case of using pdb2gmx with common forcefields, the 
constraints option can switch all or part or (h-bonds) the bonds to 
constraints, as Mark wrote.


On 11/25/2015 02:32 PM, Vedran Miletić wrote:
> Sorry, just looked deeper into this and noticed it depends on
> constraints = all-bonds option in .mdp.
> I would expect both to contain the same data? Is it written in one
> place for convenience or performance reasons, or is it something else
> entirely?
> Regards,
> Vedran
> 2015-11-25 14:00 GMT+01:00 Vedran Miletić <rivanvx at gmail.com>:
>> Hello,
>> I noticed that bonds are sometimes stored in
>> top_global->moltype->ilist[F_CONSTR] instead of
>> top_global->moltype->ilist[F_BONDS], What causes this?
>> Regards,
>> Vedran
>> --
>> Vedran Miletić
>> http://vedranmileti.ch/

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