[gmx-users] g_dist as an alternative for g_saltbr
Diogo Martins de Sá
sadiogo at mol.bio.br
Wed Oct 15 20:19:12 CEST 2014
I have read several emails exchanged in this discussion list where
g_dist is presented as a better choice for observing salt bridges in the
trajectory. And I'm totally inclined to agree with that, but that would
be the case where you already know which are the SBs present in the
system. If one has this information, he could easily create groups of
individual residues (which would actually contain just the ionazable
atoms and their hydrogens, depricating the carbons and other atoms) and
observe how the salt bridges behave.
My question is concerning the situation where you still don't know which
are the salt bridges in the system and, after that, which are the ones
you should take a closer look (I think the obvious approach would be to
search literature, but that is not always successful).
Justin Lemkul has mentioned, in two diferent discussions, using g_dist
to "track persistence of interactions" and "looping calculations" to
address the situation I've just mentioned.
Could someone elaborate on those? I am confused as to what they actually
mean and how to proceed (especially in the case of "looping
Thanks in advance,
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