There aren't any commands which allow you to calculate the distance to
specified coordinates. Probably the closest you could currently get to
this in cpptraj would be to center your system on that point via
'center point <X> <Y> <Z>', then use 'distance <mask> <mask2>', where
<mask> is your atom (or atoms) of interest and <mask2> is everything -
this way <mask2> ends up centered on your point. Does that make sense?
It sounds like interesting functionality to add to the 'distance'
command. May also be useful to add this in general to things like
'closest' - I'll have to think about this.
This all becomes much easier if you can define the point in terms of
other atoms. Any reason you can't? If you describe in more detail what
you're trying to do maybe I can think of another command that might
help.
-Dan
On Fri, Mar 31, 2017 at 10:54 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> 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/
>
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Mar 31 2017 - 08:30:02 PDT
