[gmx-users] Three molecules in single topol.top file

[Mark Abraham]

Hi,

Reading more closely I see that your error message must have come from
mdrun, whereas I assumed it was from grompp because you were talking about
topologies. Quoting boring things like command lines and GROMACS versions
is useful for getting effective help!

As it is, I can't tell whether the error comes immediately in the
simulation (which might suggest a code bug) or later on (which might
suggest you have simulation instability as the root cause). Sharing a link
to your md.log file on a file-sharing service is useful also.

Mark

On Wed, 31 Aug 2016 18:41 Chang Woon Jang <changwoonjang at gmail.com> wrote:

> Dear Mark Abraham,
>
>     I am a little confused about the meaning of "you have not taught grompp
> how to handle" (especially *taught*) because I have topology file,
> conf.gro, nonbonded and bonded force fields, grompp.mdp, index file. Do I
> need to do something else in order to specify the interaction?
>
>     What I have done is 1) reduced time-step, 2) check the initial
> configuration because the CG system actually is mapped from equilibrated
> atomistic system, 3) using -rdd options, 4) extend table-extension value.
> None of them works.
>
>     Would you give me any comments?
>
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
>
> On Wed, Aug 31, 2016 at 12:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > There's no need to use separate itp files.the include mechanism just
> pastes
> > it back in.
> >
> > The actual error message shows you have an interaction that you have not
> > taught grompp how to handle. Investigate that.
> >
> > Mark
> >
> > On Wed, 31 Aug 2016 18:12 Nikhil Maroli <scinikhil at gmail.com> wrote:
> >
> > > It is impossible to make any comments without knowing the simulation
> > > details. I hope it will help , if not provide the full details
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> > > gmx-tutorials/complex/02_topology.html
> > > --
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> --
> Best regards,
> Changwoon Jang,
>
> Postdoctoral Research Fellow
> Department of Chemical & Biological Engineering, Drexel University
> 3141 Chestnut Street, Philadelphia, PA 19104
>
> Voice: (662) 617-2267
> E-mail: cj395 at drexel.edu
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