[gmx-users] Using g_select to detect water pores in a bilayer

Teemu Murtola teemu.murtola at cbr.su.se
Thu Jan 27 18:18:01 CET 2011


On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo <m.n.melo at rug.nl> wrote:
> My idea is to count the number of water molecules within a certain z
> distance of the bilayer center, and flag a pore above a certain threshold.
> The problem is that the position of this z-slab cannot be hardcoded because
> my simulations are relatively long and there is sometimes a drift of the
> bilayer.
> also fails because the pore is lined by peptide molecules and a relatively
> large distance for the PW-C4 distance must be allowed. This means that
> interfacial waters will be frequently counted in.

This is unfortunately not possible with the current version of
g_select, as the number of available keywords is quite limited.  If
you want to do some programming, it should be relatively
straightforward (although the learning curve for the selection engine
can be quite steep) to add new keywords.  There is some documentation
in the headers selmethod.h and selparam.h, and you should be able to
implement, e.g., a selection keyword like "zwithin 0.5 of com of name
..." by looking at the existing implementations in sm_distance.c
(contains, e.g., 'within' and 'dist') and sm_simple.c (contains, e.g.,

Best regards,

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