[gmx-users] Constraining a part of the system

[HANNIBAL LECTER]

Is there a smart way of writing the constraint sections in the topology
file other than entering the values manually ?


On Tue, Sep 17, 2013 at 10:10 AM, rahul seth
<rahul.seth.gromacs at gmail.com>wrote:

> Thanks
>
>
> On Tue, Sep 17, 2013 at 10:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/17/13 10:00 AM, HANNIBAL LECTER wrote:
> >
> >> Is there a way to constraint bonds of a part of the system while keeping
> >> the other part flexible? For example for a simulation with two
> proteins, I
> >> would like to constraint the bonds of one and would like to keep the
> other
> >> flexible.
> >>
> >> I would prefer to use LINCS to constraint the system
> >>
> >>
> > Set the constraints explicitly in the topology of one protein using a
> > [constraints] directive.  Then set "constraints = none" in the .mdp file.
> >  The constraints read from the topology will override the .mdp setting
> > while leaving all other bonds unconstrained.
> >
> > -Justin
> >
> > --
> > ==============================**====================
> >
> > Justin A. Lemkul, Ph.D.
> > Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu>
> | (410)
> > 706-7441
> >
> > ==============================**====================
> >
> > --
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