[gmx-users] problem using grompp

[Sotirios Dionysios I. Papadatos]

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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