[gmx-users] Topology file

[rose rahmani]

First, i think it's better to ask WHY
http://www.gromacs.org/Documentation/How-tos/Position_Restraints
That's why people use position restraints.

About WHEN, <for example> sometimes your molecule behavior is different in
box. For instance you study the interaction of your molecule with surface.
So the molecule need to be free and move in a box to find its best
configuration toward surface. Because its properties may differ in
different part of box. You can't put a restriction on it, because it's
distance and configuration, is crucial in interacting with surface...
Maybe it's not a scientific explanation of an issue( as justin masterly do)
but i just tried to share my experience. Hope it helps!

Best

Rose



On Wed, 10 Oct 2018, 16:21 Mahdi Sobati Nezhad, <mahdisobatinezhad at gmail.com>
wrote:

> Thanks rose. Can you tell me more about which cases I should use position
> restrictions?!
> Thanks
>
> On Fri, 5 Oct 2018 10:33 rose rahmani, <rose.rhmn93 at gmail.com> wrote:
>
> > Hi,
> >
> > It depends on you, wheter you want to put position restriction on your
> > molecule you should add posre.itp to topol.top or not.
> > But whenever you use define=-DPOSRES in your .mdp file, GROMACS can read
> > posre.itp files in topol.top an apply position restriction to molecule.
> >
> > Rose
> >
> > On Fri, 5 Oct 2018, 02:24 Mahdi Sobati Nezhad, <
> > mahdisobatinezhad at gmail.com>
> > wrote:
> >
> > > Hello Gromacs users.
> > > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there
> > is
> > > no any porse.itp
> > > What can I do?!
> > > Do it's important that porse.itp should be in topol.top or its enough
> > that
> > > pdb2gmx make porse.itp?!
> > >
> > > Thanks
> > > --
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