[gmx-users] problem using grompp

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 11 11:37:49 CEST 2015


Hi,

SETTLE is a constraint algorithm for water. LINCS and SHAKE are the
available general-purpose constraint implementations - see the manual
section headed "constraint algorithms".

Mark

On Thu, Jun 11, 2015 at 10:39 AM Sotirios Dionysios I. Papadatos <
si.papadatos at edu.cut.ac.cy> wrote:

> Dear community,
>
>
> I am trying to set parameters for a molecule that doesn't exist in gromacs
> "library".
>
> I have found all the required data from the literature, apart from bond
> force constant (Kb).
>
> There seems to be a way to overcome this but using constraints on all the
> bonds using the Settle algorithm. My problem is that even by looking
> through the manual I haven't found a way to implement it. I believe I do
> know that it has to be used in the .mdp file but I don't know how.
>
> So far I have tried adding these two lines in the .mdp file:
>
> constraints=all-bonds
>
> constraint-algorithm=settle
>
> But it doesn't seem to do the trick, it still prints out the same error!
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


More information about the gromacs.org_gmx-users mailing list