[gmx-users] Issue with nrexcl (g_rdf related)

[João Henriques]

Dear all,

Please ignore my previous email. I have now realized that a bond with func.
type 1 will solve my problem and keep the model intact. It's also an
harmonic potential but considers exclusions.

Best regards,
João Henriques



On Thu, May 7, 2015 at 10:23 AM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> Dear all,
>
> A little context first: I have written my own CG bead necklace model for
> use with gromacs. Production simulations use nrexcl = 1.
>
> One of the validation analysis involves computing the rdf, and for that I
> need a .tpr with higher nrexcl, as suggested in the tool's help.
>
> Interestingly, two different .tpr files compiled using two similar
> topologies, differing only on the nrexcl, produce similar outputs when
> checked with gmxdump (the init. velocities differ but that's normal,
> because the seed is random).
>
> Needless to say that rdf outputs are similar regardless of which .tpr I
> use (they are the same!).
>
> I double checked that the .top files differ uniquely on the nrexcl value.
>
> Tested with gmx-4.6.7 and gmx-5.0.4.
>
> P.S.: I use an harmonic potential for the bonds (func. type 6). Don't know
> if this matters, but I have a feeling it does.
>
> Thank you for your attention,
> Best regards,
> João Henriques
>