Thanks Hannes!
Alternatively I could just find the closest water oxygen (that could work
for restarts too) and use that instead of the coordinates in the
restraintmask. Is this possible with cpptraj? I know that the "distance"
command calculates the distance between the COM of two selections, it
doesn't return the closest atoms to a point.
best
Thomas
On 31 March 2017 at 15:35, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
wrote:
> Hi Thomas,
>
> On Fri, 31 Mar 2017 15:13:37 +0200
> Thomas Evangelidis <tevang3.gmail.com> wrote:
>
> > Is it possible to have coordinates in the restraint mask? For example
> > I want to restrain all atoms that are within 8 Angstroms from a point
> > in 3D space:
> >
> > restraintmask="! ( ( -13.5541 3.4173 15.1382 ) <: 8.0) )"
>
> I think you would need to do this with an actual atom at those
> coordinates (maybe even introduce a dummy atom if really necessary).
> And this will be only static that is the mask would be only computed
> once at the start of the simulations, so you would have to think what
> you want to do in case of restarts.
>
>
> Cheers,
> Hannes.
>
>
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--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Fri Mar 31 2017 - 08:00:02 PDT
