[gmx-users] g_select position variables
cara_a_k at hotmail.com
Fri Aug 1 07:42:24 CEST 2014
I suspected that might have been the case. It would be good to see a "z of" option in a future version, if you find the time.
> Date: Thu, 31 Jul 2014 20:47:11 +0300
> From: teemu.murtola at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_select position variables
> On Tue, Jul 29, 2014 at 6:18 AM, Cara Kreck <cara_a_k at hotmail.com> wrote:
> > Is it possible to use a position variable in conjunction with x,y,z
> > keywords in g_select?
> Unfortunately, this is currently not possible.
> I'm trying to select all molecules within a channel embedded in a membrane.
> > In case the protein and/or membrane moves around I want to use position
> > variables instead of numerical values to define the z range. I've tried
> > this in my selection.dat file:
> > solution = resname SOL or resname CL;
> > top = res_com of resnr 1181;
> > bottom = res_com of resnr 55;
> > cavity = solution and z bottom to top;
> > cavity;
> > and
> > cavity = solution and z<top and z>bottom;
> > cavity;
> > But I get an invalid selection error. However, if I substitute top and
> > bottom with numbers, it does work. Is there something wrong with my syntax
> > or am I just trying to do the impossible?
> Yes, this is as expected. There is currently no way to generate single
> numbers from position-valued expressions like "top" and "bottom" above. It
> may be difficult to implement either of the above syntaxes, but what could
> be relatively easy is that one could write "z of top" to extract a number
> which could then be used in comparisons. But it may take time before I get
> around to implementing anything like this.
> Best regards,
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