[gmx-users] g_dist as an alternative for g_saltbr

[Justin Lemkul]

On 10/15/14 2:19 PM, Diogo Martins de Sá wrote:
> Fellow users,
>
>
> 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
> calculations").
>

Likely I was referring to looping over calls to g_dist (in the future, please 
link to any previous discussions - it's hard for me to keep track of all of the 
thousands of messages I've sent :)

One can certainly use g_saltbr to look at positive-negative interactions en 
masse, but it's a fairly "dumb" program, in that it considers a huge amount of 
groups that don't matter.  You can weed through all of that to find things that 
might be of interest.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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