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

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 A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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