Dear Users, My polypeptide has 90 residues. I divided them into 5 type of beads. For example lets take the example of basic residues (type B) - I have Lysine, Arginine and Histidine and acidic (A) only one Aspartic Acid and one Glutmaic acid so two in total. I wish to assign different mass to each of them but they belong to the one type.
How I can I specify this in gromacs topology so Votca will calculate RDF after each step between e.g. A and B? Another issue: potential between Acidic - Acidic. As i have two Acidic residues only I specify RDF between A1 and A2. But then Votca will calculate RDF between A-A so twoA-twoA which I do not wan to. If specify them separately so two types A1 and A2 instead of type A Votca will calculate wrongly A1-B and A2 - B and I wish to have A-B. Would you advise? Steven -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
