[gmx-users] Intermolecular interactions in RDF

[Justin Lemkul]

On 12/10/19 12:37 AM, Apramita Chand wrote:
> Dear All,
> I have 10 peptides in my system and I want to calculate the peptide-peptide
> radial distribution function.
> How can I calculate only the intermolecular interactions amongst the
> peptides (excluding the intramolecular peaks) without repeating the entire
> simulation?
> The manual has two options for this: setting -nrexcl or giving -cut option
> But I am confused as to what values could be specified for such systems?

The value of nrexcl would have to be set to the longest run of 
contiguous bonds in the molecule.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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