[gmx-users] Martini force field - coarse grained protein tutorials

[David Ackerman]

Hello,

I am also attempting to run Martini using version 5 and am getting the same
two errors with an mdp file that worked (aside from warnings) on version
4.6.5. Does anyone have a solution to this problem?

-David

On Mon, Sep 15, 2014 at 3:37 AM, Sridhar Kumar Kannam <srisriphy at gmail.com>
wrote:

> Hi Tsjerk,
>
> Thank you. I missed those links.
>
> Now when I minimize the system (protein in vacuum) I am getting the
> following errors. I am using 5.0 version.
>
> ERROR 1 [file minimization-vaccum.mdp]:
>   With Verlet lists only cut-off, reaction-field, PME and Ewald
>   electrostatics are supported
>
> ERROR 2 [file minimization-vaccum.mdp]:
>   Explicit switch/shift coulomb interactions cannot be used in combination
>   with a secondary coulomb-modifier.
>
>
> Can you please explain them ...
>
>
> Thanks again.
>
>
>
>
>
>
> On Mon, Sep 15, 2014 at 5:23 AM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Sridhar,
> >
> > Have you tried clicking on the .mdp file names in the commands, which are
> > underlined and highlighted in blue? Seems to work for me.
> >
> > Cheers,
> >
> > Tsjerk
> > On Sep 14, 2014 12:41 PM, "Sridhar Kumar Kannam" <srisriphy at gmail.com>
> > wrote:
> >
> > > Hi All,
> > >
> > > I am a newbie to Gromacs and Martini force field. I begin with the
> > > tutorials - http://md.chem.rug.nl/cgmartini/index.php/proteins
> > >
> > > As this tutorial does not provide the .mdp files I have tried to built
> > the
> > > .mdp files based on other Gromacs tutorials. But when I run the
> > simulations
> > > I am getting different kinds of error. As I have not read the manual
> yet,
> > > its hard to debug the errors. Can someone please share the *mdp files
> to
> > > run this tutorial (Ubiquitin and HIV-Prtease) simulations.
> > >
> > > Thank you.
> > >
> > >
> > >
> > >
> > > --
> > > Cheers !!!
> > > Sridhar  Kumar Kannam :)
> > > --
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>
> --
> Cheers !!!
> Sridhar  Kumar Kannam :)
> --
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