On 11/14/13 10:18 PM, bharat gupta wrote:
Hi,

How can I calculate the average number of salt bridges between two residues
during the entire simulation ??...


Unless you've got some wildly noncanonical residues, this is a binary function. Either the salt bridge exists (1) or does not (0). You can define a salt bridge a number of ways, but the easiest and most common is the distance between the COM of the positive and negative moieties. Use g_dist over time and post-process the output to determine the fraction of time spent within the distance cutoff; it's a much more useful quantity.

-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
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jalem...@outerbanks.umaryland.edu | (410) 706-7441

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