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

[Sridhar Kumar Kannam]

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 :)