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

[Chang Woon Jang]

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