[gmx-users] Three molecules in single topol.top file
Chang Woon Jang
changwoonjang at gmail.com
Wed Aug 31 18:41:00 CEST 2016
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?
On Wed, Aug 31, 2016 at 12:31 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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.
> 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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