[gmx-users] LINCS WARNING Error in running production run in parallel of a MARTINI SYSTEM of membrane protein

[Tsjerk Wassenaar]

Hi Antara,

What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.

Cheers,

Tsjerk

On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar <antara.mazumdar at igib.in>
wrote:

> Dear users,
>
> I am trying to run a coarse grained simulation of a membrane protein in a
> mixed lipid billayer using martini model 2.2. I have already performed all
> the equilibration steps successfully on my desktop with GROMACS 5.1.0.
> However, when i try to execute its production run in parallel(having
> gromacs 5.1 version installed)  it complains of LINCS warning and
> terminates at step 0. But on the contrary, it runs on the desktop
> successfully. Kindly suggest something and please let me know if any more
> information is required from my side.
>
>
> Thanks!!
>
> Kind Regards,
> Antara
>
> --
> Junior research fellow(project)
> Systems biology group
> CSIR-Institute of Genomics & Integrative Biology
> South Campus
> New Delhi -  110020
> M : +91-9717970040
> --
>
>
>
> On Fri, May 13, 2016 at 11:11 PM, Antara mazumdar <antara.mazumdar at igib.in
> >
> wrote:
>
> > Dear gromacs users,
> >
> > I am trying to run a coarse grained simulation of a membrane protein in a
> > mixed lipid billayer using martini model. I have already performed all
> the
> > equilibration steps successfully on my desktop. However, when i try to
> > execute its production run in parallel it complains of LINCS warning and
> > terminates at step 0. But on the contrary, it runs on the desktop
> > successfully. Kindly suggest something and please let me know if any more
> > information is required from my side.
> >
> >
> > Thanks!!
> >
> >
> >
> > Kind Regards,
> > Antara
> >
> > --
> > Junior research fellow(project)
> > Systems biology group
> > CSIR-Institute of Genomics & Integrative Biology
> > South Campus
> > New Delhi -  110020
> > M : +91-9717970040
> > --
> >
> >
> >
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.