[gmx-users] problem using grompp

[Mark Abraham]

Hi,

Yes, there is no need or use for a force constant if the bond is rigid
(though IIRC you'll need to give grompp a dummy number anyway)

Mark

On Thu, Jun 11, 2015 at 11:51 AM Sotirios Dionysios I. Papadatos <
si.papadatos at edu.cut.ac.cy> wrote:

> Thanks for your quick reply, so it a fact that I can bypass the missing
> bonds force constant field in grompp by using these constraints?
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mark
> Abraham <mark.j.abraham at gmail.com>
> Sent: Thursday, June 11, 2015 12:37 PM
> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] problem using grompp
>
> 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!
> > --
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