[gmx-users] Average number of salt bridge

[Justin Lemkul]

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
School of Pharmacy
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University of Maryland, Baltimore
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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