2013/7/11 <[email protected]>: > 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. Tristan is right, masses have no influence on the rdfs. The argument is pretty much the same as why Monte Carlo gives you the right rdfs, too (without knowing the masses).
> > How I can I specify this in gromacs topology so Votca will calculate RDF > after each step between e.g. A and B? I don't understand your question. VOTCA calculates the rdf of all interactions listed in the settings xml file once the simulations is done. You can do that by hand too, just run csg_stat yourself. > > > 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. You can use the special type A*, which matches the names A1 and A2. > > 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. > > -- Christoph Junghans Web: http://www.compphys.de -- 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.
