Hi Steven, Any equilibrium thermodynamic quantity, such as a RDF, cannot depend on the masses of the system (they only couple to the particle velocities, not to the interaction potentials). So your calculation cannot depend on the beads' masses. Look out for masses only if you're interested in dynamics.
Best, Tristan On Thu, Jul 11, 2013 at 1:45 PM, <[email protected]> wrote: > 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. > > -- 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.
