[gmx-users] Regarding calculation of Salt bridge between specific group of atoms

[Justin A. Lemkul]

bipin singh wrote:
> Dear all,
> 
> I want to calculate the salt bridge interaction between a particular
> set of residues,
> because I can not use index file with g_saltbr, so the next options
> available are
> g_dist and g_mindist. As stated in manual g_dist gives the  distance between the
> center of mass of two groups of atom, while g_mindist gives us the minimum
> distance between any pair of atom.
> My doubt is that which distance(either given by g_dist or g_mindist)
> corresponds to the salt bridge interaction distance
> between two atoms.

Not necessarily either.  g_dist measures COM distances between the given index 
groups, and g_mindist measures the minimum distance of any atom pair, which, for 
a multi-atom index group, may change over time.

The solution is to create specific index groups.  If you want the distance 
between two specific atoms, create two index groups of one atom each and use 
g_dist (or g_mindist, because in this case the output would be identical).  If 
you want the distance between, e.g. the amino group of lysine and the 
carboxylate of glutamate, then the amine group with have four atoms (NZ, HZ1, 
HZ2, HZ3) and the carboxylate group will have 3 (CD, OE1, OE2).  Then use g_dist.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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