[gmx-users] multiple peptide simulation

[Apramita Chand]

Dear All,
If I have multiple peptides in my system and want to calculate
inter-peptide hydrogen bonds, should I group all the peptides separately
and calculate hydrogen bonds between every pair of peptide and sum them up?
Or calculate overall no. of hydrogen bonds choosing the generic 'Protein'
option from index file and divide by no. of peptides?

If its the former option, once we obtain a average no of h-bonds between
two peptides, should we divide by half?


Another question along similar lines is that if we carry out dssp analysis
and we want to find out overall percentage of various secondary structures
in the peptides, what option should we select in the index file? The
generic 'Protein' option chooses all the peptides together. So if we choose
that, the last line of scout.xvg (obtained from dssp) would show some
percentage values. Is it for the overall system as I wanted?

Please advise.


Yours sincerely,
Apramita