Thank you both! I run the first iteration and I got my RDFs in step 001 with RDF values app. 100 times bigger than the original submitted... Do you have any clue? Is that the number of frames I used which is bigger?
W dniu czwartek, 11 lipca 2013 15:33:14 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/11 <[email protected] <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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.
